Contacts of the strand formed by residues 34 - 39 (chain Y) in PDB entry 4MXV
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 ILE 34 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Y LEU* 4.6 4.0 - - + -
22Y CYS* 4.4 9.6 - - + -
24Y ALA* 4.3 9.2 - - + -
27Y TYR* 3.5 24.2 - - - +
29Y PHE* 3.9 21.5 - - + -
32Y TYR 4.4 2.9 - - - +
33Y VAL* 1.3 81.1 - - - +
35Y HIS* 1.3 72.8 + - - +
36Y TRP* 4.1 8.7 + - - +
50Y TYR* 3.4 4.6 - - - -
51Y ASN* 3.2 30.2 + - + +
52Y PRO* 5.0 3.6 - - - -
69Y ILE* 4.9 0.2 - - - +
78Y ALA* 4.0 25.1 - - + +
92Y CYS* 4.1 17.5 - - + -
93Y SER 3.7 9.9 - - - +
94Y ARG* 4.5 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 35 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X TRP* 3.6 19.5 - + - -
33Y VAL* 4.8 0.6 - - + +
34Y ILE* 1.3 77.5 - - - +
36Y TRP* 1.3 62.2 + - - +
37Y VAL* 4.2 1.3 - - + -
47Y TRP* 3.0 22.7 + - + +
49Y GLY 3.5 2.9 - - - -
50Y TYR* 3.3 32.4 - + + +
92Y CYS* 3.2 5.4 - - - -
93Y SER* 2.7 50.8 + - - +
95Y PRO* 3.9 14.9 - - + +
98Y LEU* 2.8 32.2 + - + +
100Y PHE* 3.5 28.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Y GLU* 4.1 14.1 - - - -
20Y LEU* 3.8 32.3 - - + -
21Y SER 4.0 3.8 - - - -
22Y CYS* 3.9 26.5 - - + -
34Y ILE* 4.1 6.1 + - - +
35Y HIS* 1.3 77.6 + - - +
37Y VAL* 1.3 64.7 + - - +
47Y TRP* 3.9 1.4 - - - -
48Y VAL* 2.8 43.3 + - + -
49Y GLY 2.8 10.3 + - - -
69Y ILE* 3.4 41.7 - - + +
78Y ALA* 3.9 17.7 - - + +
79Y TYR 3.7 5.9 + - - -
80Y LEU* 3.6 37.5 - - + -
90Y TYR* 4.7 6.7 - - + -
91Y TYR 3.3 18.6 - - - -
92Y CYS* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98X PHE* 4.3 3.1 - - + -
35Y HIS* 4.2 6.0 - - + -
36Y TRP* 1.3 79.5 - - - +
38Y ARG* 1.3 68.7 + - - +
45Y LEU* 4.1 18.4 - - + -
46Y GLU 3.3 15.9 - - - +
47Y TRP* 4.0 13.7 - - + -
48Y VAL* 4.3 0.9 - - - -
90Y TYR* 4.7 1.1 - - - -
91Y TYR* 2.8 41.9 + - + +
92Y CYS* 5.0 0.2 - - - +
93Y SER* 5.5 2.5 - - - -
100Y PHE* 3.7 32.1 - - + -
103Y TRP* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y VAL* 1.3 76.6 - - - +
39Y GLN* 1.3 66.0 + - - +
40Y ALA 5.2 0.7 - - - +
44Y GLY 3.8 0.3 - - - +
45Y LEU* 3.4 2.1 - - - -
46Y GLU* 2.7 65.0 + - + +
48Y VAL* 4.1 6.6 - - + +
62Y LYS* 3.7 10.7 - - - +
63Y PHE* 3.2 37.5 - - - -
67Y PHE* 4.3 2.4 - - - -
85Y GLU* 4.3 10.6 + - - +
86Y ASP* 3.0 33.2 + - - +
88Y ALA* 4.4 6.9 - - + +
89Y VAL 3.4 6.7 - - - +
90Y TYR* 2.9 52.1 + - + -
91Y TYR* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X GLN* 3.1 40.4 + - - -
87X TYR* 3.6 9.3 + - - -
38Y ARG* 1.3 78.7 - - - +
40Y ALA* 1.3 66.0 + - - +
41Y PRO* 3.7 0.9 - - - +
42Y GLY 5.8 0.7 - - - +
43Y LYS 3.2 27.1 + - - +
44Y GLY 3.3 8.5 - - - +
45Y LEU* 3.7 23.2 - - + +
88Y ALA* 3.4 3.6 - - - -
89Y VAL* 2.9 37.2 + - + +
91Y TYR* 3.8 16.0 + - + -
----------------------------------------------------------
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