Contacts of the strand formed by residues 33 - 42 (chain B) in PDB entry 1MS4
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 SER 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.5 3.2 - - - +
32B HIS* 1.3 105.3 + - - +
34B PHE* 1.3 65.5 - - - +
35B ARG* 4.2 0.4 - - - -
53B ARG* 2.9 36.3 + - - +
57B SER* 3.5 23.5 - - - -
363B VAL* 3.5 1.6 - - - -
364B TYR* 3.0 32.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
11B PHE* 3.5 52.7 - + + +
12B LYS 3.8 22.4 - - - -
13B ARG* 4.5 2.5 - - - -
16B SER* 4.0 20.0 - - - -
18B VAL* 4.2 9.0 - - + -
31B VAL* 3.3 44.6 - - + -
33B SER* 1.3 75.0 - - - +
35B ARG* 1.3 60.6 + - - +
51B ASP 3.3 15.7 - - - +
52B ALA* 4.1 9.4 - - + -
66B VAL* 3.9 9.2 - - + -
68B LYS* 5.8 0.7 - - - -
357B GLU* 4.5 0.2 - - - +
364B TYR* 3.1 26.7 + - - +
366B LEU* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 4.2 1.1 - - - -
34B PHE* 1.3 80.0 - - - +
36B LEU* 1.3 69.1 + - + +
37B PRO* 3.6 2.9 - - - -
50B ALA* 3.4 5.5 - - - +
51B ASP* 3.1 26.2 + - + +
53B ARG* 3.9 48.2 - - - +
57B SER 5.0 1.7 + - - -
59B ASP* 4.7 5.7 + - - -
314B ARG* 3.5 26.3 - - - +
341B ALA* 4.3 1.4 - - - +
342B TYR* 3.7 21.1 + - - -
357B GLU* 2.7 38.4 + - - +
364B TYR* 3.4 52.7 + - + -
366B LEU* 4.4 2.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
35B ARG* 1.3 79.2 - - + +
37B PRO* 1.3 76.3 - - - +
38B ALA* 4.5 2.3 - - - +
49B ILE 3.6 8.8 - - - +
50B ALA* 3.8 3.8 - - - -
51B ASP* 2.9 37.2 - - - +
53B ARG* 3.5 12.3 - - - +
96B ASP* 3.1 30.5 - - - +
97B PRO* 4.5 11.5 - - + +
179B ALA* 3.8 28.5 - - + -
180B GLY 5.3 1.8 + - - +
230B GLU* 5.2 2.7 - - - +
286B GLN* 5.0 3.1 - - + -
342B TYR* 3.6 30.1 - - + -
357B GLU* 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG 3.6 2.4 - - - -
36B LEU* 1.3 93.7 - - - +
38B ALA* 1.3 61.4 + - - +
49B ILE 3.8 5.4 - - - +
180B GLY* 4.0 10.2 - - - -
286B GLN* 4.7 2.7 + - - +
342B TYR* 3.5 21.1 - - + +
343B SER* 3.6 23.2 - - - +
344B SER* 3.6 8.4 - - - -
355B LEU* 3.5 43.3 - - + +
357B GLU* 4.1 6.7 - - + -
366B LEU* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 4.5 2.5 - - - +
37B PRO* 1.3 76.4 - - - +
39B LEU* 1.3 59.3 + - - +
40B VAL* 4.2 2.1 - - - +
47B VAL 3.6 1.7 - - - +
48B ALA* 3.5 3.1 - - - -
49B ILE* 2.9 41.8 + - + +
97B PRO 4.8 2.9 - - - +
99B VAL* 4.0 16.8 - - + -
180B GLY* 3.8 29.6 - - - +
181B VAL* 4.0 4.9 - - + -
344B SER* 3.5 6.3 - - - -
355B LEU* 4.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 1.3 72.2 - - - +
40B VAL* 1.3 67.4 + - - +
46B MET* 3.7 23.3 - - + -
47B VAL 3.6 16.4 - - - +
48B ALA* 4.4 10.3 - - + -
77B TRP* 4.5 0.9 - - + -
181B VAL* 3.9 4.3 - - - +
344B SER* 2.8 30.9 + - - +
345B VAL 4.6 4.0 - - - +
346B LEU* 3.4 38.5 - - + +
353B TYR* 4.0 8.1 - - + -
355B LEU* 3.9 28.7 - - + +
368B PHE* 4.0 22.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
38B ALA 5.0 1.3 - - - +
39B LEU* 1.3 82.2 - - - +
41B ASN* 1.3 60.3 + - - +
42B VAL* 4.2 2.9 - - + -
46B MET* 3.5 4.0 - - - +
47B VAL* 2.9 47.0 + - + +
49B ILE* 5.4 1.3 - - + -
99B VAL* 4.2 11.0 - - + -
101B VAL* 3.7 28.3 - - + -
106B LEU* 3.8 21.8 - - + -
181B VAL* 3.8 31.9 - - + -
346B LEU* 4.2 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 1.3 76.7 - - - +
42B VAL* 1.3 60.2 + - - +
43B ASP* 4.0 2.5 + - - +
44B GLY* 2.9 40.7 + - - +
45B VAL 3.3 3.6 + - - +
46B MET* 4.7 0.7 - - - +
101B VAL* 3.7 17.7 - - - +
346B LEU* 4.1 17.7 - - + +
347B TYR 5.8 0.4 + - - +
348B LYS* 3.8 31.8 - - + +
349B ASP* 5.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.1 1.1 - - + -
41B ASN* 1.3 74.8 + - - +
43B ASP* 1.3 70.7 + - + +
44B GLY 3.2 0.4 - - - -
45B VAL* 2.9 29.0 + - - +
47B VAL* 4.1 9.0 - - + -
101B VAL* 4.0 15.0 - - + -
103B GLY 3.5 21.1 - - - +
104B ASN* 3.7 14.8 - - - -
105B LYS 4.5 0.4 - - - +
106B LEU* 3.6 38.1 - - + -
138B VAL* 3.6 27.6 - - + +
----------------------------------------------------------
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