Contacts of the helix formed by residues 13 - 33 (chain B) in PDB entry 3VOD
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 PRO 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLY 6.1 1.1 - - - +
120A HIS* 4.8 9.4 - - + -
136A GLU* 3.8 4.3 - - - +
11B ILE* 4.3 5.1 - - + +
12B ILE* 1.4 92.6 - - + +
14B LEU* 1.3 66.2 + - - +
15B GLY 3.3 4.2 + - - +
16B ARG* 3.4 41.8 + - + +
17B LEU* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A HIS* 3.9 18.3 - - + +
123A LEU* 4.3 17.3 - - + -
124A THR* 3.7 26.2 - - + -
132A VAL* 5.2 2.5 - - + +
135A LEU* 3.7 29.6 - - + -
136A GLU* 3.2 26.8 + - + +
139A LEU* 3.5 31.2 - - + -
13B PRO* 1.3 73.0 - - - +
15B GLY* 1.3 63.3 + - - +
17B LEU* 3.3 4.5 + - - +
18B ILE* 3.0 38.1 + - + +
142B VAL* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.2 29.4 - - - +
119A LEU* 4.5 11.7 - - - -
120A HIS* 5.0 2.8 - - - -
123A LEU* 4.5 13.7 - - - +
13B PRO* 3.3 3.0 - - - +
14B LEU* 1.3 79.0 - - - +
16B ARG* 1.3 60.4 + - - +
18B ILE* 3.6 1.8 + - - +
19B HIS* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 4.5 28.1 + - + -
12B ILE* 4.5 15.2 - - + +
13B PRO* 3.4 43.6 + - - +
14B LEU 3.3 0.4 - - - -
15B GLY* 1.3 73.9 - - - +
17B LEU* 1.3 60.7 + - - +
19B HIS* 3.2 9.8 + - + +
20B MET* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 3.5 42.2 - - + +
139A LEU* 4.1 14.6 - - + -
140A LYS* 3.9 21.3 - - + +
143A LEU* 3.8 24.0 - - + -
12B ILE* 3.8 40.8 - - + +
13B PRO 3.3 8.6 + - - +
14B LEU 3.3 7.7 + - - +
16B ARG* 1.3 78.3 - - - +
18B ILE* 1.3 57.6 + - - +
20B MET* 3.3 5.9 + - - +
21B VAL* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.3 9.9 - - + +
21A VAL* 3.4 28.5 - - + +
22A ASN* 3.6 38.6 - - + +
25A LYS* 4.5 4.9 - - + -
123A LEU* 4.9 6.7 - - + -
135A LEU* 5.6 0.4 - - + -
139A LEU* 4.0 15.3 - - + -
14B LEU* 3.0 46.6 + - + +
15B GLY* 3.8 6.3 - - - +
17B LEU* 1.3 77.1 - - - +
19B HIS* 1.3 57.1 + - - +
21B VAL* 3.9 5.0 - - - +
22B ASN* 2.9 28.6 + - - +
139B LEU* 4.6 10.1 - - + -
142B VAL* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 3.8 15.8 + - - -
25A LYS* 4.2 10.2 + - - +
44A LYS* 4.6 25.2 + - + -
15B GLY 3.2 13.5 + - - +
16B ARG* 3.2 13.6 + - + +
18B ILE* 1.3 76.9 - - - +
20B MET* 1.3 64.6 + - + +
22B ASN* 3.3 5.9 + - - +
23B GLN* 3.0 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.8 36.7 - - + +
12B ILE* 5.2 11.2 - - + -
16B ARG* 2.9 30.0 + - + +
17B LEU* 3.3 9.6 + - - +
19B HIS* 1.3 81.6 - - + +
21B VAL* 1.3 62.1 + - - +
23B GLN* 3.3 10.0 + - - +
24B LYS* 3.1 23.4 + - - +
27B ARG* 5.2 1.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
18A ILE* 3.4 33.2 - - + -
139A LEU* 3.7 36.1 - - + +
142A VAL* 3.8 22.7 - - + -
143A LEU* 3.8 18.8 - - + -
17B LEU 2.9 23.7 + - - +
18B ILE* 4.0 4.9 - - - +
20B MET* 1.3 75.0 - - - +
22B ASN* 1.3 57.3 + - - +
24B LYS* 3.5 4.6 + - - +
25B LYS* 3.0 27.4 + - - +
123B LEU* 4.6 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.6 17.0 - - + +
19A HIS* 4.0 13.7 - - - -
22A ASN* 3.3 32.3 + - - +
18B ILE 2.9 19.4 + - - +
19B HIS* 3.4 7.7 + - - +
20B MET 3.3 0.2 - - - -
21B VAL* 1.3 74.3 - - - +
23B GLN* 1.3 63.5 + - - +
25B LYS* 3.1 28.7 + - - +
26B ASP* 3.0 38.7 + - - +
44B LYS* 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL 3.9 19.2 + - - -
64A LEU* 5.5 4.2 + - - +
65A SER* 5.6 4.9 + - - -
19B HIS* 3.0 43.8 + - + +
20B MET* 3.3 11.8 + - - +
22B ASN* 1.3 78.3 - - - +
24B LYS* 1.3 56.9 + - - +
26B ASP* 3.1 10.9 + - - +
27B ARG* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 2.5 38.9 + - + +
143A LEU* 4.5 13.2 - - + +
144A PRO 3.7 17.9 + - - -
20B MET 3.1 13.2 + - - +
21B VAL* 3.6 8.5 - - - +
23B GLN* 1.3 72.2 - - - +
25B LYS* 1.3 65.1 + - - +
27B ARG* 3.2 26.3 + - - +
28B LEU* 3.0 36.1 + - + +
122B GLU* 4.5 6.6 + - - -
123B LEU* 4.0 28.0 + - + +
125B LYS* 5.1 8.2 - - - +
126B ASN* 5.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 3.1 35.4 + - - +
18A ILE* 4.4 7.4 - - + -
19A HIS* 4.2 11.3 - - - +
21B VAL 3.0 14.1 + - - +
22B ASN* 3.2 32.5 - - - +
24B LYS* 1.3 76.2 - - - +
26B ASP* 1.3 78.3 + - - +
28B LEU* 3.5 2.8 + - - +
29B LEU* 2.9 42.7 + - + +
44B LYS* 3.9 10.3 - - - +
119B LEU* 3.8 17.5 - - + +
123B LEU* 4.2 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.0 23.1 + - - +
23B GLN* 3.1 12.0 + - - +
25B LYS* 1.3 103.5 + - - +
27B ARG* 1.3 64.3 + - - +
29B LEU* 3.2 7.6 + - - +
30B ASN* 3.0 32.7 + - - +
40B ALA* 4.0 7.4 - - + +
44B LYS* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET 5.2 1.4 + - - -
23B GLN* 2.9 30.9 + - - +
24B LYS* 3.4 30.1 - - + +
26B ASP* 1.3 75.8 - - - +
28B LEU* 1.3 65.9 + - + +
30B ASN* 3.3 9.6 + - - +
31B GLU* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 3.0 24.4 + - + +
27B ARG* 1.3 78.5 - - + +
29B LEU* 1.3 66.1 + - - +
31B GLU* 3.1 22.9 + - - +
32B TYR* 2.8 40.5 + - + +
119B LEU* 3.5 26.7 - - + -
122B GLU* 3.4 40.4 - - + +
123B LEU* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 2.9 42.1 + - + +
26B ASP* 3.2 16.1 + - - +
28B LEU* 1.3 75.4 - - - +
30B ASN* 1.3 63.2 + - - +
32B TYR* 3.2 3.3 + - - +
33B LEU* 2.9 42.2 + - + +
40B ALA* 3.7 16.8 - - + -
43B PHE* 4.3 19.5 - - + -
44B LYS* 4.6 7.2 - - + -
115B VAL* 3.5 37.7 - - + -
119B LEU* 4.0 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.0 23.8 + - - +
27B ARG* 3.5 10.5 - - - +
28B LEU 3.3 0.2 - - - -
29B LEU* 1.3 75.1 - - - +
31B GLU* 1.3 62.4 + - - +
33B LEU* 4.0 3.4 - - - +
34B SER* 3.3 21.5 + - - -
38B ILE 4.9 1.2 - - - +
39B THR* 3.3 17.4 - - - +
40B ALA* 2.9 34.7 + - - +
41B ALA 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG 3.1 11.8 + - - +
28B LEU* 3.1 31.4 + - - +
30B ASN* 1.3 75.7 - - - +
32B TYR* 1.3 70.4 + - + +
34B SER* 3.1 26.3 - - - -
35B PRO* 3.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 2.8 55.7 + - + +
29B LEU* 4.8 0.2 - - - -
31B GLU* 1.3 83.7 + - + +
33B LEU* 1.3 57.6 + - - +
34B SER 3.3 0.2 - - - -
35B PRO* 3.6 6.0 - - - +
114B LEU* 3.4 29.3 - - - +
115B VAL* 3.6 24.9 - - + +
118B ASP* 3.5 36.9 + - + +
119B LEU* 3.9 22.2 - - + -
122B GLU* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.9 31.8 + - + +
30B ASN 4.2 1.8 - - - +
32B TYR* 1.3 76.2 - - - +
34B SER* 1.3 64.6 + - - +
35B PRO* 3.3 2.9 - - - -
36B LEU* 3.0 18.3 + - + +
37B ASP 3.7 2.3 + - - -
38B ILE* 3.2 26.0 - - + +
39B THR 3.8 3.6 - - - +
40B ALA* 3.8 20.4 - - - +
43B PHE* 3.7 29.2 - - + -
111B CYS* 3.6 40.8 - - + -
114B LEU* 4.6 4.0 - - + -
115B VAL* 3.6 17.5 - - + -
----------------------------------------------------------
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