Contacts of the strand formed by residues 34 - 39 (chain P) in PDB entry 3KYM
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 MET 34 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P LEU* 4.8 7.6 - - - -
22P CYS* 5.8 0.7 - - - -
27P PHE* 3.9 20.9 - - + -
29P PHE* 3.6 33.0 - - + -
32P TYR* 4.0 10.5 - - + +
33P PRO* 1.3 82.1 - - - +
35P PHE* 1.3 62.9 + - - +
50P TRP* 3.3 5.4 - - - -
51P ILE* 3.0 31.7 + - + +
70P ILE* 4.2 2.4 - - - +
72P ARG* 3.5 14.1 - - - +
79P LEU* 3.5 33.7 - - + -
96P CYS* 5.4 2.0 - - - -
97P ALA 4.7 2.5 - - - -
98P ARG* 3.4 39.0 - - + -
99P GLU* 3.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O TRP* 6.1 1.1 - + - -
96O LEU* 3.7 23.6 - - + -
34P MET* 1.3 75.1 - - - +
36P TRP* 1.3 65.5 + - - +
47P TRP* 3.4 26.0 - + - -
49P SER 3.2 19.7 - - - -
50P TRP* 3.5 27.1 - + + -
70P ILE* 5.0 0.2 - - - -
79P LEU* 3.8 7.2 - - - +
95P TYR 4.1 0.2 - - - -
96P CYS* 3.3 6.8 - - - -
97P ALA* 3.1 35.9 + - + -
98P ARG 4.1 4.8 - - - +
99P GLU* 2.8 41.1 - - + -
104P TRP* 4.4 12.1 - + + -
105P TYR 4.7 4.0 - - - -
106P PHE* 3.2 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLU* 4.4 11.9 - - + -
20P LEU* 3.7 33.7 - - + -
21P SER 4.2 3.4 - - - -
22P CYS* 4.1 17.9 - - + -
35P PHE* 1.3 72.0 - - - +
37P VAL* 1.3 64.5 + - - +
47P TRP* 4.4 0.3 - - - -
48P VAL* 3.1 27.4 + - + -
49P SER* 3.2 23.0 + - - +
70P ILE* 3.4 27.3 - - + +
79P LEU* 3.4 36.3 - - + +
80P TYR 3.5 8.9 + - - -
81P LEU* 3.3 43.1 - - + +
94P TYR* 4.4 10.5 - - + -
95P TYR 3.0 41.5 - - - -
96P CYS* 4.0 5.2 - - - -
113P THR* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O PHE* 4.1 11.4 - - + -
35P PHE* 4.5 2.0 - - + -
36P TRP* 1.3 79.5 - - - +
38P ARG* 1.3 74.4 + - - +
45P LEU* 4.5 5.4 - - + -
46P GLU 3.8 12.3 - - - +
47P TRP* 4.1 6.1 - - - -
48P VAL* 3.7 4.9 - - - -
94P TYR* 3.3 3.6 - - - +
95P TYR* 2.6 43.0 + - + +
97P ALA* 4.8 2.5 - - + -
106P PHE* 3.7 36.6 - - + -
109P TRP* 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P VAL* 1.3 78.8 - - - +
39P GLN* 1.3 61.6 + - - +
40P ALA 4.4 0.4 - - - +
45P LEU* 3.6 1.9 - - - -
46P GLU* 2.8 75.5 + - + +
48P VAL* 3.4 23.6 - - + +
63P SER* 4.9 3.4 + - - -
64P VAL* 4.5 18.8 - - - +
68P PHE* 4.9 4.7 - - - -
89P GLU* 3.4 13.4 + - - +
90P ASP* 2.8 47.4 + - - +
92P ALA* 4.3 8.7 - - + +
93P THR 3.4 5.2 - - - +
94P TYR* 3.6 30.6 + - + -
95P TYR* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O GLN* 2.9 37.9 + - - +
87O TYR* 3.7 5.3 + - - -
38P ARG* 1.3 76.9 - - - +
40P ALA* 1.3 66.3 + - - +
41P PRO* 3.8 0.7 - - + -
42P GLY 5.4 0.7 - - - -
43P LYS 3.2 22.8 + - - +
44P GLY 3.5 13.3 - - - -
45P LEU* 3.3 22.9 - - + +
46P GLU* 5.4 0.2 - - - -
92P ALA* 3.0 3.8 - - - +
93P THR* 2.9 44.3 + - + +
95P TYR* 4.1 16.8 + - + -
----------------------------------------------------------
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