Contacts of the helix formed by residues 50 - 60 (chain B) in PDB entry 1WOH
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 PHE 50 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 2.9 21.4 + - - +
49B ARG* 1.3 84.9 - - + +
51B ALA* 1.3 61.1 - - - +
52B PRO* 3.4 1.8 - - - -
53B ARG* 3.3 22.3 + - + +
54B ALA* 3.1 21.0 + - - +
277B PRO* 4.1 10.5 - - + -
278B ASN* 5.3 8.3 - - + +
9D TYR* 3.4 31.6 - - + -
44E PHE* 3.8 27.1 - + - -
45E ARG* 4.0 19.1 - - + -
46E PRO* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY 3.9 1.2 + - - -
48B ALA 2.9 11.9 + - - +
50B PHE* 1.3 75.8 - - - +
52B PRO* 1.3 64.9 - - - +
54B ALA* 3.1 0.5 + - - +
55B LEU* 2.8 30.7 + - + +
118B GLY 3.1 22.4 - - - +
275B LEU* 3.3 38.1 - - + +
277B PRO* 3.8 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY* 4.2 2.5 - - - -
36B VAL 4.0 7.9 - - - +
37B PRO* 4.0 10.5 - - + -
48B ALA 3.5 2.9 - - - +
49B ARG 3.5 14.8 - - - +
50B PHE 3.5 0.7 - - - -
51B ALA* 1.3 89.5 - - + +
53B ARG* 1.3 61.8 + - - +
55B LEU* 3.4 2.4 + - - +
56B ARG* 3.1 47.5 + - - +
85B ASP* 4.0 11.2 - - - +
117B LEU* 3.2 39.7 - - + +
118B GLY 3.2 12.1 - - - +
119B GLY 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 5.5 1.6 - - + -
49B ARG 5.4 0.4 + - - +
50B PHE* 3.3 22.1 + - + +
51B ALA 3.2 0.6 - - - -
52B PRO* 1.3 80.9 - - - +
54B ALA* 1.3 62.6 + - - +
56B ARG* 3.2 13.4 + - - +
57B GLU* 3.1 42.2 + - + +
8D PRO 3.3 27.9 + - - -
9D TYR* 3.4 26.3 + - - +
10D GLY 3.5 1.0 + - - -
11D GLY 3.0 27.5 + - - -
13D PRO* 4.0 15.6 - - + +
57D GLU* 3.6 34.4 + - - +
60D LEU* 3.5 17.2 - - - +
44E PHE* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE 3.1 8.2 + - - +
51B ALA 3.1 2.0 + - - +
53B ARG* 1.3 77.1 - - - +
55B LEU* 1.3 57.8 + - - +
57B GLU* 3.4 13.3 + - - +
58B ALA* 2.9 30.1 + - - +
275B LEU* 4.5 0.7 - - + -
277B PRO* 3.3 39.0 - - + -
286B GLU* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.1 5.9 - - + -
51B ALA* 2.8 32.7 + - + +
52B PRO 3.8 3.4 - - - +
54B ALA* 1.3 71.6 - - - +
56B ARG* 1.3 59.8 + - - +
58B ALA* 3.4 4.1 + - - +
59B SER* 2.8 31.6 + - - -
117B LEU* 4.0 37.7 - - + -
118B GLY 4.6 1.6 - - - +
272B LEU* 3.8 25.8 - - + +
275B LEU* 4.6 7.9 - - + -
286B GLU* 4.1 11.4 - - - +
289B MET* 4.1 14.6 - - + +
290B ALA* 3.8 32.7 - - - +
293B VAL* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.5 30.1 - - + +
14B THR 4.0 1.4 - - - +
15B PHE* 3.7 19.5 - - + +
33B ALA 5.2 0.2 - - - -
34B LEU* 4.5 1.6 - - - +
35B GLY 3.7 6.7 - - - +
52B PRO* 3.1 37.5 + - - +
53B ARG* 3.2 12.9 + - - +
55B LEU* 1.3 74.4 - - - +
57B GLU* 1.3 63.6 + - - +
59B SER* 2.5 25.5 + - - -
60B LEU* 3.6 9.9 + - - +
82B ASP* 2.9 30.6 + - - -
84B GLY* 2.9 21.8 + - - -
85B ASP* 2.9 37.2 + - - -
117B LEU* 4.4 10.9 - - + +
11D GLY 5.2 1.8 + - - -
12D ILE* 3.2 17.8 - - - +
13D PRO* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 4.9 1.4 - - - +
13B PRO* 3.6 25.0 - - + +
53B ARG* 3.1 26.1 + - - +
54B ALA* 3.7 12.3 - - - +
56B ARG* 1.3 77.0 - - - +
58B ALA* 1.3 61.8 + - - +
60B LEU* 3.1 24.4 + - - +
61B ARG* 4.4 1.7 + - - +
44C PHE* 5.8 3.0 - - - -
53D ARG* 3.8 27.7 + - - +
57D GLU* 2.4 30.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 2.9 18.5 + - - +
55B LEU 3.8 0.9 - - - +
57B GLU* 1.3 77.1 - - - +
59B SER* 1.3 61.0 + - - +
61B ARG* 3.1 23.9 + - - +
62B SER* 4.0 2.1 + - - -
286B GLU* 3.4 40.2 - - + +
287B LEU* 3.7 19.9 - - + +
290B ALA* 3.6 10.3 - - + +
44C PHE* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.7 1.7 + - - -
15B PHE* 3.6 19.6 - - - -
16B ALA* 2.9 30.5 + - - -
55B LEU 2.8 14.8 + - - -
56B ARG 2.5 21.7 + - - -
58B ALA* 1.3 71.7 - - - +
60B LEU* 1.3 53.6 + - - +
61B ARG 3.0 6.1 - - - -
62B SER* 2.7 38.1 + - - +
63B VAL* 3.5 2.9 + - - +
290B ALA* 3.7 9.6 - - - +
294B MET* 5.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.4 38.3 - - + +
10B GLY 4.0 2.7 - - - +
12B ILE 4.7 0.7 - - - +
13B PRO* 4.3 13.2 - - + -
14B THR 3.8 18.8 - - - +
17B ARG* 3.6 58.0 + - + +
56B ARG 3.7 6.1 - - - +
57B GLU 3.3 15.5 - - - +
58B ALA 3.1 1.0 - - - -
59B SER* 1.3 77.4 - - - +
61B ARG* 1.3 58.4 + - - +
62B SER 3.2 1.6 - - - -
63B VAL* 3.6 15.5 - - - +
185C ARG* 5.4 0.3 + - - -
53D ARG* 3.5 21.8 - - - +
----------------------------------------------------------
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