Contacts of the helix formed by residues 12 - 34 (chain B) in PDB entry 5DIR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 12 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.1 37.1 + - + +
11B PRO* 1.3 76.8 - - - +
13B LEU* 1.3 56.1 + - - +
14B TRP 3.1 1.3 - - - -
15B ILE* 3.1 53.3 + - + +
88B LEU* 4.3 13.9 - - + -
96B THR* 4.0 34.1 - - + -
99B ALA* 3.8 25.9 - - + +
100B ILE* 3.5 34.1 - - + -
103B ALA* 3.5 8.4 - - + +
204B OLC 3.3 69.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 2.9 33.4 + - + +
11B PRO 2.9 1.2 + - - -
12B TRP* 1.3 73.0 - - - +
14B TRP* 1.3 60.3 + - - +
15B ILE 3.1 2.0 - - - -
16B THR* 3.1 13.9 + - + +
17B VAL* 2.9 30.5 + - - +
85B VAL* 5.0 14.4 - - + -
88B LEU* 3.5 27.4 - - + -
106B LEU* 3.7 28.3 - - + -
205B OLC 4.4 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 2.9 32.6 + - + +
13B LEU* 1.3 76.2 - - - +
15B ILE* 1.3 60.7 + - - +
17B VAL* 3.8 20.9 - - + +
18B LEU* 2.8 29.9 + - - +
204B OLC 5.5 8.5 - - + -
205B OLC 3.2 93.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.1 45.0 + - + +
13B LEU 3.1 0.2 - - - -
14B TRP* 1.3 76.4 - - - +
16B THR* 1.3 59.2 + - - +
18B LEU* 3.2 6.6 + - - +
19B VAL* 2.8 38.3 + - + +
100B ILE* 4.2 19.1 - - + +
103B ALA* 3.8 13.9 - - + -
104B LEU* 4.2 24.5 - - + +
204B OLC 3.8 48.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.1 20.7 + - + +
15B ILE* 1.3 78.8 - - - +
17B VAL* 1.3 60.9 + - + +
19B VAL 3.4 0.2 + - - -
20B PHE* 2.9 28.5 + - + +
103B ALA* 3.0 33.8 + - - +
106B LEU* 3.7 26.2 - - + +
107B GLY* 3.7 23.5 - - - +
110B LEU* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 2.9 20.5 + - - +
14B TRP* 3.8 20.2 - - + +
16B THR* 1.3 78.2 - - + +
18B LEU* 1.3 59.0 + - - +
20B PHE* 3.2 7.3 + - + +
21B VAL* 2.9 34.9 + - + +
205B OLC 3.6 65.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TRP 2.8 19.0 + - - +
15B ILE* 3.6 6.3 - - + +
17B VAL* 1.3 77.8 - - - +
19B VAL* 1.3 60.8 + - - +
21B VAL* 3.6 6.8 + - + +
22B LEU* 3.1 48.6 + - + +
204B OLC 3.9 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 2.8 26.6 + - + +
16B THR* 3.7 4.0 - - - +
18B LEU* 1.3 69.7 - - - +
20B PHE* 1.3 66.7 + - - +
22B LEU* 3.3 3.3 + - - +
23B ASP* 2.9 26.5 + - + +
104B LEU* 3.9 26.2 - - + -
107B GLY* 3.6 20.6 - - - +
108B GLY* 3.7 2.0 - - - +
141B LEU* 5.2 1.2 - - + +
142B ALA* 5.2 1.6 - - - -
145B ALA* 3.6 25.6 - - + -
204B OLC 3.7 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 2.9 18.6 + - + +
17B VAL* 3.2 8.0 + - + +
19B VAL* 1.3 76.8 - - - +
21B VAL* 1.3 69.0 + - + +
23B ASP* 3.3 4.5 + - - +
24B GLN* 3.0 46.2 + - + +
107B GLY* 4.1 10.3 + - - +
110B LEU* 3.5 30.5 - - + -
111B GLY* 3.8 20.6 - - - -
114B TYR* 3.8 29.6 - + + -
205B OLC 4.0 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.9 33.9 + - + +
18B LEU* 3.9 7.6 - - + +
20B PHE* 1.3 77.1 - - + +
22B LEU* 1.3 66.6 + - + +
24B GLN* 3.0 6.4 + - - +
25B VAL* 2.9 41.0 + - + +
205B OLC 4.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.1 41.8 + - + +
19B VAL* 3.8 3.6 - - - +
21B VAL* 1.3 79.7 - - + +
23B ASP* 1.3 56.9 + - - +
25B VAL* 3.1 21.0 - - + +
26B SER* 2.5 28.9 + - - -
141B LEU* 4.3 13.2 - - + -
204B OLC 3.8 23.6 - - + -
207B OLC 3.7 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 2.9 19.9 + - + +
20B PHE* 3.4 7.2 - - - +
21B VAL 3.2 0.2 - - - -
22B LEU* 1.3 77.8 - - - +
24B GLN* 1.3 72.1 + - - +
26B SER* 3.3 3.2 - - - -
27B LYS* 2.8 64.1 + - - +
107B GLY 5.5 0.2 - - - +
111B GLY* 3.4 9.1 - - - -
140B ASN* 4.1 0.2 - - - +
141B LEU* 3.8 14.5 + - + +
142B ALA* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.0 32.5 + - + +
21B VAL* 3.0 7.2 + - - +
23B ASP* 1.3 83.6 + - - +
25B VAL* 1.3 60.4 + - - +
26B SER 3.2 0.2 - - - -
27B LYS* 3.5 9.5 + - - +
28B ALA* 2.9 29.9 + - - +
111B GLY* 2.8 33.7 + - - -
114B TYR* 3.7 29.3 - - + +
115B ASP* 3.7 14.3 + - - +
205B OLC 5.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 2.9 28.1 + - + +
22B LEU* 3.1 36.6 - - + +
24B GLN* 1.3 72.7 - - - +
26B SER* 1.3 59.6 + - - +
28B ALA* 3.4 6.2 + - - +
29B PHE* 2.9 32.3 + - - +
207B OLC 5.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 2.5 21.4 + - - -
23B ASP* 3.3 8.1 - - - -
25B VAL* 1.3 79.0 - - - +
27B LYS* 1.3 62.0 + - - +
29B PHE* 3.2 6.4 + - - +
30B PHE* 3.1 30.3 + - - -
125B PHE* 3.4 28.7 - - - -
141B LEU* 3.4 16.7 - - - +
207B OLC 3.5 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 2.8 44.4 + - - +
24B GLN* 4.0 12.3 - - - +
26B SER* 1.3 76.2 - - - +
28B ALA* 1.3 66.7 + - - +
30B PHE* 3.3 0.9 + - - -
31B GLN* 3.0 32.8 + - - +
111B GLY 3.4 4.9 + - - -
112B ASN* 2.8 25.7 + - - -
115B ASP* 2.7 33.2 + - - +
122B VAL* 4.3 0.2 - - - +
123B VAL* 3.4 28.3 - - + +
125B PHE* 3.9 13.7 - - + -
140B ASN* 3.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN 2.9 19.5 + - - +
25B VAL* 3.7 7.2 - - - +
27B LYS* 1.3 77.6 - - - +
29B PHE* 1.3 62.7 + - - +
31B GLN* 3.6 12.4 + - - +
32B ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 2.9 18.2 + - - +
26B SER* 3.4 6.1 - - - +
27B LYS 3.2 0.2 - - - -
28B ALA* 1.3 77.5 - - - +
30B PHE* 1.3 96.0 + + - +
32B ALA* 2.9 8.5 + - - +
33B GLU* 2.8 56.8 + - + +
207B OLC 4.0 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 3.1 25.3 + - - +
27B LYS 4.3 1.6 - - - +
29B PHE* 1.3 101.4 - + - +
31B GLN* 1.3 64.7 + - - +
33B GLU 3.9 1.6 - - - +
34B LEU* 3.1 52.2 + - + +
49B TRP* 3.4 50.5 - + + -
50B THR 4.3 4.5 - - - +
51B LEU* 3.7 8.8 - - + +
123B VAL* 5.7 0.2 - - + -
125B PHE* 3.4 47.3 - + + -
207B OLC 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.0 25.8 + - - +
28B ALA* 3.8 9.6 - - - +
30B PHE* 1.3 76.9 - - - +
32B ALA* 1.3 60.4 + - - +
34B LEU 3.5 10.0 - - - +
51B LEU* 4.0 13.1 - - + +
53B TYR* 3.9 20.6 + - - +
119B LEU* 3.7 19.1 - - - +
121B HIS* 4.9 1.2 - - - -
123B VAL* 3.4 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.1 16.6 + - - +
29B PHE* 2.9 7.4 + - - +
31B GLN* 1.3 79.7 - - - +
33B GLU* 1.3 67.6 + - + +
34B LEU 3.8 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 2.8 52.0 + - + +
32B ALA* 1.3 83.3 - - + +
34B LEU* 1.3 77.0 + - + +
38B GLN* 4.4 5.7 + - - +
207B OLC 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.1 35.1 + - + +
31B GLN 3.5 10.0 - - - +
32B ALA 4.7 1.0 - - - -
33B GLU* 1.3 99.3 - - + +
35B SER* 1.3 66.9 + - - +
38B GLN* 3.5 17.7 - - - +
40B ILE* 3.7 29.2 - - + -
49B TRP* 4.2 6.5 - - + +
50B THR* 3.4 43.5 - - - +
51B LEU* 3.2 19.0 - - + +
207B OLC 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il