Contacts of the strand formed by residues 32 - 39 (chain J) in PDB entry 4KRM
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 TYR 32 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I LEU* 4.0 15.1 - - - +
1J GLN* 4.8 0.5 - - - +
2J VAL* 3.3 34.8 - - + +
27J ARG 3.9 6.6 + - - -
28J THR* 4.6 6.3 - - - -
30J ARG* 3.3 36.8 + - + +
31J SER* 1.3 77.2 - - - +
33J GLY* 1.3 53.8 + - - +
34J MET* 4.0 15.0 - - - -
53J TRP* 3.4 10.0 - - - -
72J ARG* 2.7 40.8 + - - +
98J ALA* 3.7 15.0 - - + -
99J ALA 3.4 4.3 - - - -
100J ALA* 3.5 33.0 - - + -
101J GLY 2.9 4.8 + - - -
113J TYR* 3.5 29.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J TYR* 1.3 71.6 - - - +
34J MET* 1.3 60.3 + - - -
51J ILE 3.4 11.2 - - - -
98J ALA* 3.5 1.6 - - - -
99J ALA* 2.8 42.4 + - - +
101J GLY 3.2 5.7 + - - -
102J SER 3.9 5.8 - - - -
103J ALA 3.2 22.7 - - - -
104J TRP* 4.8 1.3 - - - -
111J TYR* 3.8 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J LEU* 4.0 13.5 - - + -
22J CYS* 4.5 0.4 - - - -
24J ALA* 5.3 5.6 - - + -
32J TYR* 4.0 14.6 - - - -
33J GLY* 1.3 73.8 - - - -
35J GLY* 1.3 58.4 + - - +
50J GLY* 3.3 1.7 - - - -
51J ILE* 2.8 45.3 + - + +
70J ILE* 4.5 0.8 - - - +
72J ARG* 3.6 24.9 - - - +
79J VAL* 4.0 26.2 - - + -
96J CYS* 3.8 22.9 - - - -
97J ALA 3.3 15.3 - - - +
98J ALA* 3.7 24.9 - - + -
104J TRP* 4.1 0.3 - - - +
111J TYR* 4.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J MET* 1.3 75.1 - - - +
36J TRP* 1.3 66.8 + - - +
37J PHE* 4.2 6.1 - - - -
49J SER 3.3 10.3 - - - -
50J GLY* 4.1 0.2 - - - -
79J VAL* 5.9 0.2 - - - +
95J TYR 3.8 0.2 - - - +
96J CYS* 3.6 5.7 - - - -
97J ALA 2.8 33.8 + - - +
111J TYR* 3.5 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J GLU* 4.0 30.7 - - + -
20J LEU* 3.6 42.8 - - + -
21J THR 4.1 5.6 - - - -
22J CYS* 3.7 26.0 - - + -
35J GLY* 1.3 75.5 - - - -
37J PHE* 1.3 66.3 + - - +
47J PHE* 4.1 0.7 - - - -
48J VAL* 2.9 26.2 + - + -
49J SER* 2.7 21.3 + - - +
70J ILE* 3.8 22.9 - - + -
79J VAL* 3.8 20.7 - - + +
80J ASP 4.0 7.9 + - - -
81J LEU* 3.7 36.9 - - + +
94J TYR* 4.1 12.3 - - + -
95J TYR 3.4 19.1 - - - -
96J CYS* 4.0 5.2 - - + -
118J THR* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J GLY 4.3 3.8 - - - -
36J TRP* 1.3 79.9 - - - +
38J ARG* 1.3 58.0 + - - +
45J ARG* 4.1 11.0 - - + -
46J GLU* 3.3 9.0 - - - +
47J PHE* 3.4 42.8 - + + -
48J VAL* 3.9 3.4 - - - -
94J TYR* 3.3 7.3 - - - +
95J TYR* 2.6 38.0 + - + +
97J ALA* 4.0 11.0 - - + -
107J THR 3.8 1.6 - - - -
108J LEU* 3.4 30.7 - - + -
111J TYR* 3.5 42.8 - + - -
114J TRP* 3.5 36.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J PHE* 1.3 75.2 - - - +
39J GLN* 1.3 62.1 + - - +
40J ALA* 4.3 1.7 + - + +
44J GLU 4.0 0.7 - - - +
45J ARG* 3.5 3.6 - - - -
46J GLU* 2.9 61.0 + - + +
48J VAL* 3.5 15.9 - - + +
63J SER* 3.3 27.5 + - - -
64J VAL* 4.1 14.7 - - - +
68J PHE* 4.3 1.0 - - - -
89J GLU* 4.3 9.3 + - - +
90J ASP* 3.0 34.8 + - - +
92J ALA* 3.9 10.3 - - + -
93J ILE 3.1 11.9 - - - +
94J TYR* 2.9 42.9 + - + -
95J TYR* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468I SER* 5.3 8.1 + - - -
38J ARG* 1.3 74.8 - - - +
40J ALA* 1.3 64.1 + - - +
41J PRO* 3.9 1.1 - - + +
43J LYS 3.4 24.3 + - - +
44J GLU* 4.0 3.9 - - - +
45J ARG* 3.5 46.6 + - + +
92J ALA* 3.4 3.4 - - - -
93J ILE* 2.9 31.6 + - + +
95J TYR* 3.9 19.7 + - + +
----------------------------------------------------------
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