Contacts of the helix formed by residues 23 - 36 (chain B) in PDB entry 4U1D
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 GLU 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 2.9 28.4 + - + +
21B VAL* 4.4 16.0 - - + +
22B GLY* 1.3 78.8 - - - +
24B LYS* 1.3 62.7 + - - +
25B GLN 3.3 2.5 - - - -
26B ALA* 3.2 20.7 + - + +
27B ALA* 3.1 17.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
19B ILE* 3.9 34.8 - - + +
22B GLY* 3.2 15.6 + - - +
23B GLU* 1.3 74.5 - - - +
25B GLN* 1.3 59.8 + - - +
27B ALA* 3.1 10.6 + - - +
28B LEU* 2.9 26.9 + - - +
58B ILE* 4.4 3.6 - - + +
61B GLU* 6.0 3.8 - - - +
62B LEU* 4.0 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU 3.3 0.6 - - - -
24B LYS* 1.3 78.8 - - - +
26B ALA* 1.3 57.9 + - - +
28B LEU* 3.2 4.8 + - + +
29B GLN* 2.9 32.1 + - + +
62B LEU* 4.1 14.1 - - + +
64B LYS* 3.3 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.1 13.7 - - + +
23B GLU* 3.2 27.9 + - + +
25B GLN* 1.3 77.5 - - - +
27B ALA* 1.3 57.2 + - - +
29B GLN* 4.0 5.8 - - - +
30B SER* 3.1 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.6 28.0 - - + +
18B LEU* 3.6 16.3 - - + +
19B ILE* 3.6 18.2 - - + -
23B GLU 3.1 7.2 + - - +
24B LYS 3.1 10.1 + - - +
26B ALA* 1.3 75.5 - - - +
28B LEU* 1.3 63.3 + - - +
30B SER* 2.4 25.6 + - - -
31B LEU* 3.2 10.9 + - - +
58B ILE* 4.7 4.0 - - + -
----------------------------------------------------------
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 2.9 8.9 + - - +
25B GLN* 3.2 9.6 + - + +
27B ALA* 1.3 76.8 - - - +
29B GLN* 1.3 64.0 + - - +
31B LEU* 3.2 4.3 + - - +
32B HIS* 3.1 19.1 + - - +
55B PHE* 3.4 47.8 - - + +
58B ILE* 3.4 27.0 - - + +
59B GLY* 3.7 19.7 - - - +
62B LEU* 3.9 10.5 - - + -
64B LYS* 3.8 23.8 - - + -
67B LEU* 3.7 22.9 - - + -
68B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 2.9 20.0 + - + +
26B ALA* 4.2 6.1 - - - +
28B LEU* 1.3 77.2 - - - +
30B SER* 1.3 60.7 + - - +
32B HIS* 3.4 18.0 + - - +
33B ASP* 3.1 52.9 + - - +
67B LEU* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 5.2 1.6 + - - -
14B ARG* 5.8 2.5 - - - +
15B ALA* 4.7 5.5 + - - +
18B LEU* 4.3 12.1 - - - +
26B ALA 3.1 18.0 + - - -
27B ALA* 2.4 26.1 + - - -
29B GLN* 1.3 77.0 - - - +
31B LEU* 1.3 64.7 + - - +
33B ASP* 3.2 21.0 + - - +
34B PHE* 3.3 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.9 30.1 - - + +
12B ILE* 4.4 3.4 - - - +
15B ALA* 4.0 8.1 - - + -
27B ALA 3.2 7.2 + - - +
28B LEU* 3.2 8.8 + - - +
30B SER* 1.3 79.5 + - - +
32B HIS* 1.3 67.2 + - - +
34B PHE* 3.0 14.5 + - + +
35B ILE* 3.0 17.8 + - - +
51B VAL* 3.6 23.8 - - + -
54B LYS* 3.4 29.4 - - + -
55B PHE* 3.6 26.9 - - + +
58B ILE* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 3.1 9.8 + - - +
29B GLN* 3.4 29.4 - - - +
31B LEU* 1.3 76.2 - - - +
33B ASP* 1.3 60.5 + - - +
35B ILE* 3.4 3.5 + - - -
36B THR* 2.7 59.8 + - + +
55B PHE* 3.6 29.2 - - + -
67B LEU* 3.4 28.1 - - + +
70B ASP* 3.2 27.9 + - - -
71B GLY* 3.7 11.8 - - - -
74B GLN* 4.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 3.1 35.4 + - - +
30B SER* 3.3 14.3 - - - +
31B LEU 3.2 0.6 - - - -
32B HIS* 1.3 79.7 - - - +
34B PHE* 1.3 62.4 + - - +
36B THR* 3.9 5.0 + - - -
37B ALA* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.5 36.8 - - + -
7B ARG 4.1 11.9 - - - -
8B PRO* 3.8 24.5 - - + -
11B ALA* 4.0 16.2 - - + -
30B SER 3.3 7.4 + - - +
31B LEU* 3.0 13.7 + - - +
33B ASP* 1.3 80.9 - - - +
35B ILE* 1.3 63.8 + - + +
37B ALA* 3.4 19.1 - - - +
39B ARG* 4.1 20.2 - - - -
40B ILE* 3.4 11.6 - - + +
48B VAL* 4.1 16.8 - - + -
51B VAL* 3.4 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.0 11.4 + - - +
32B HIS* 3.6 6.7 - - - +
34B PHE* 1.3 79.3 - - + +
36B THR* 1.3 64.3 + - + +
37B ALA 3.3 1.0 + - - -
40B ILE* 3.8 8.8 - - - +
48B VAL* 4.7 3.4 - - + -
51B VAL* 3.5 32.8 - - + +
52B VAL* 3.6 37.0 - - + +
55B PHE* 3.4 38.8 - - + -
71B GLY* 4.2 18.2 - - - +
75B TYR* 3.7 23.6 - - + +
78B LEU* 3.8 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 2.7 53.4 + - + +
33B ASP* 3.9 5.1 + - - -
35B ILE* 1.3 87.9 - - + +
37B ALA* 1.3 64.8 + - - +
38B ARG* 3.8 3.1 + - - +
71B GLY 4.1 7.9 - - - +
74B GLN* 3.6 43.0 + - + -
75B TYR 4.6 0.2 - - - +
78B LEU* 3.7 13.0 - - - +
----------------------------------------------------------
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