Contacts of the helix formed by residues 31 - 45 (chain B) in PDB entry 1W4R
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 GLY 31 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 3.3 23.1 - - - -
42A ARG* 4.7 1.3 - - - +
29B PHE 3.3 1.4 + - - -
30B SER* 1.3 80.5 - - - +
32B LYS* 1.3 64.9 + - - +
33B SER 3.3 3.1 - - - -
34B THR* 3.2 9.7 + - - -
35B GLU* 3.0 18.9 + - - +
149B LEU* 4.0 1.1 - - - -
300B TTP 2.9 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.9 8.3 - - + +
25B LEU 3.7 11.0 - - - +
26B GLY* 3.5 18.8 - - - +
27B PRO 3.0 17.4 + - - -
30B SER* 3.3 12.7 - - - +
31B GLY* 1.3 73.3 - - - +
33B SER* 1.3 57.2 + - - +
35B GLU* 3.3 2.9 + - - +
36B LEU* 2.9 28.4 + - - +
122B ALA* 3.8 17.3 - - + +
123B ALA* 3.4 38.6 - - - +
124B LEU* 3.6 4.4 - - - +
149B LEU* 3.8 11.4 - - + -
300B TTP 2.7 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 1.3 77.3 - - - +
34B THR* 1.3 58.8 + - - +
36B LEU* 3.4 8.2 + - - +
37B MET* 3.0 33.5 + - - +
62B SER 5.9 2.5 - - - -
63B SER* 5.7 4.6 - - - -
97B ASP* 2.6 36.6 + - - -
300B TTP 3.2 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.8 22.2 - - + +
38A ARG* 3.7 27.8 - - + -
41A ARG* 3.9 23.4 + - - +
31B GLY* 3.2 13.8 + - - -
33B SER* 1.3 76.6 - - - +
35B GLU* 1.3 59.9 + - - +
37B MET* 3.2 6.7 + - - +
38B ARG* 2.8 28.1 + - - +
41B ARG* 6.0 0.2 - - - +
300B TTP 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.7 15.0 - - - +
38A ARG* 4.1 6.4 - - - +
24B ILE* 3.8 16.8 - - + -
31B GLY 3.0 13.0 + - - +
32B LYS 3.7 7.4 - - - +
34B THR* 1.3 72.2 - - - +
36B LEU* 1.3 66.3 + - - +
38B ARG* 2.9 39.3 + - - +
39B ARG* 2.8 59.8 + - - +
149B LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 9.3 - - + +
32B LYS 2.9 13.0 + - - +
33B SER* 3.5 9.2 - - - +
35B GLU* 1.3 76.7 - - - +
37B MET* 1.3 63.2 + - - +
39B ARG* 3.3 2.9 + - - +
40B VAL* 3.0 36.3 + - + +
52B VAL* 4.7 8.5 - - + -
95B GLY* 3.8 14.4 - - - -
96B ILE 3.6 29.8 - - - +
97B ASP* 3.9 18.2 - - + +
120B ILE* 3.4 40.6 - - + +
122B ALA* 4.1 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 3.0 20.8 + - - +
34B THR* 3.2 6.3 + - - +
36B LEU* 1.3 79.4 - - + +
38B ARG* 1.3 67.5 + - - +
40B VAL* 4.4 3.1 - - + +
41B ARG* 2.9 64.7 + - - +
52B VAL* 3.8 29.6 - - + -
65B PHE* 6.3 3.6 - - + -
73B MET* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER 2.8 28.9 + - - +
31A GLY* 3.3 35.4 - - - +
34A THR* 3.8 14.8 - - + -
35A GLU* 4.1 18.1 + - - +
149A LEU* 3.7 25.7 - - - +
150A THR 4.5 1.2 + - - +
34B THR 2.8 17.8 + - - +
35B GLU* 2.9 46.7 + - - +
37B MET* 1.3 73.3 - - - +
39B ARG* 1.3 74.7 + - - +
41B ARG* 3.9 6.7 - - - +
42B ARG* 3.2 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 3.0 42.9 + - - +
23B VAL 4.8 1.2 + - - +
24B ILE* 3.7 18.9 - - - +
35B GLU* 2.8 42.7 + - - +
36B LEU 3.7 4.0 - - - +
37B MET 3.2 0.2 - - - -
38B ARG* 1.3 85.8 - - - +
40B VAL* 1.3 62.9 + - - +
42B ARG* 3.3 23.2 + - - +
43B PHE* 3.2 22.5 - - + -
120B ILE* 3.8 20.6 - - + +
145B SER* 4.3 8.8 + - - -
147B VAL* 3.7 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.0 37.8 + - + +
37B MET* 3.9 8.3 - - + +
39B ARG* 1.3 77.2 - - - +
41B ARG* 1.3 61.8 + - - +
43B PHE* 3.0 20.4 + - - +
44B GLN* 3.0 9.9 + - - +
50B CYS* 3.8 29.1 - - + -
51B LEU 5.4 0.7 - - - +
52B VAL* 4.3 8.7 - - + -
73B MET* 3.9 21.8 - - + -
93B VAL* 4.4 6.1 - - + -
95B GLY* 4.3 13.7 - - - +
120B ILE* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.0 26.6 + - - +
34B THR* 6.0 0.2 - - - +
37B MET* 2.9 63.2 + - + +
38B ARG* 3.9 5.7 - - - +
40B VAL* 1.3 73.6 - - - +
42B ARG* 1.3 65.8 + - - +
44B GLN* 3.7 12.2 - - + +
45B ILE* 2.9 28.1 + - - +
65B PHE* 4.9 16.4 - - - -
73B MET* 4.3 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE 3.9 17.7 - - - +
30A SER 4.0 8.5 - - - +
31A GLY* 5.5 0.2 - - - -
150A THR* 3.0 47.0 + - - -
151A ALA* 3.3 18.3 + - - +
152A VAL* 3.7 27.3 + - + +
159A GLU* 4.5 7.9 + - - +
22B GLN* 5.6 3.6 - - - +
38B ARG* 3.2 38.8 + - - +
39B ARG* 3.4 15.7 + - - +
40B VAL 3.2 0.2 - - - -
41B ARG* 1.3 77.4 - - - +
43B PHE* 1.3 88.2 + - - +
45B ILE* 3.2 20.6 - - - +
46B ALA 3.8 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 4.0 14.8 - - + -
157A PHE 5.9 1.8 - - - -
20B GLN* 5.6 3.1 - - - -
22B GLN* 4.9 7.0 - - - -
39B ARG* 3.2 24.9 - - + -
40B VAL 3.0 6.5 + - - +
42B ARG* 1.3 97.8 - - - +
44B GLN* 1.3 65.1 + - - +
46B ALA* 3.0 10.4 + - - -
47B GLN 3.3 0.3 + - - -
48B TYR* 3.1 62.6 + + + -
50B CYS* 4.3 1.6 - - - -
93B VAL* 3.8 25.6 - - + -
118B THR* 4.2 21.8 - - + -
120B ILE* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL 3.0 14.5 + - - +
41B ARG* 3.7 14.3 - - - +
43B PHE* 1.3 77.3 - - - +
45B ILE* 1.3 66.6 + - - +
47B GLN* 3.0 27.4 + - - +
48B TYR 3.9 13.2 + - - +
50B CYS* 3.9 14.5 - - + -
73B MET* 4.3 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.2 25.8 - - + +
152A VAL 6.0 1.3 - - - +
154A MET* 3.8 31.3 - - + +
178A ALA* 4.8 12.8 - - + -
183A SER* 5.8 0.2 - - - +
41B ARG 2.9 13.7 + - - +
42B ARG* 3.2 22.0 - - - +
44B GLN* 1.3 84.2 + - - +
46B ALA* 1.3 56.7 + - + +
47B GLN* 3.3 12.0 + - - +
----------------------------------------------------------
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