Contacts of the strand formed by residues 34 - 39 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.9 15.7 - - + -
22F CYS* 4.5 4.7 - - - -
24F ALA* 5.0 2.0 - - + -
27F TYR* 3.3 25.8 - - - +
29F PHE* 4.7 9.2 - - + -
32F TYR 4.6 3.8 - - - +
33F VAL* 1.3 77.1 - - - +
35F HIS* 1.3 72.7 + - - +
36F TRP* 4.1 8.4 - - - +
50F TYR* 3.3 6.2 - - - -
51F ASN* 3.1 30.4 + - + +
52F PRO* 5.4 1.6 - - - -
69F ILE* 4.9 0.2 - - - +
78F ALA* 3.8 30.1 - - + -
92F CYS* 4.2 13.5 - - + -
93F SER 3.6 4.7 - - - +
94F ARG* 3.9 20.2 - - + +
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Residues in contact with HIS 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E TRP* 3.8 11.7 - + - -
33F VAL* 4.7 0.9 - - + +
34F ILE* 1.3 78.6 - - - +
36F TRP* 1.3 67.8 + - - +
37F VAL* 4.8 1.1 - - + -
47F TRP* 3.1 21.3 + - + +
49F GLY 3.4 4.0 - - - +
50F TYR* 3.6 27.6 - + + +
92F CYS* 3.3 5.9 - - - -
93F SER* 2.7 49.3 + - - +
95F PRO* 3.9 19.4 - - + +
98F LEU* 3.0 31.3 + - + +
100F PHE* 3.3 34.1 - + + -
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Residues in contact with TRP 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLU* 3.8 19.3 - - - -
20F LEU* 3.9 29.6 - - + -
21F SER 4.1 16.6 - - - -
22F CYS* 4.0 16.6 - - + -
34F ILE* 4.1 10.6 - - - +
35F HIS* 1.3 80.5 + - - +
37F VAL* 1.3 62.7 + - - +
47F TRP* 3.9 1.2 - - - -
48F VAL* 2.9 46.4 + - + +
49F GLY 2.9 10.2 + - - +
69F ILE* 3.6 38.6 - - + +
78F ALA* 4.0 6.6 - - + +
79F TYR 3.8 6.9 + - - -
80F LEU* 3.6 37.0 - - + -
90F TYR* 4.4 8.3 - + + -
91F TYR 3.4 19.1 - - - -
92F CYS* 4.0 11.0 - - + -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PHE* 4.5 4.0 - - + -
35F HIS* 4.8 4.0 - - + -
36F TRP* 1.3 80.1 - - - +
38F ARG* 1.3 61.2 + - - +
45F LEU* 4.0 29.2 - - + -
46F GLU 3.3 17.0 - - - +
47F TRP* 4.4 7.4 - - + -
48F VAL* 4.5 0.4 - - - -
90F TYR* 4.7 1.6 - - - -
91F TYR* 2.7 44.5 + - - +
93F SER* 5.0 2.9 - - - -
100F PHE* 3.8 36.1 - - + -
103F TRP* 3.9 23.1 - - + -
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Residues in contact with ARG 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 1.3 75.6 - - - +
39F GLN* 1.3 64.6 + - - +
40F ALA 5.2 0.9 - - - +
44F GLY 4.0 0.2 - - - +
45F LEU* 3.6 2.6 - - - -
46F GLU* 2.8 62.4 + - + +
48F VAL* 4.1 6.4 - - + +
62F LYS* 4.7 9.1 - - - +
63F PHE* 3.5 33.6 - - - -
66F ARG* 5.2 0.2 - - - +
67F PHE* 4.0 4.2 - - - -
83F ARG* 5.9 0.6 - - - +
85F GLU* 4.1 16.7 + - - +
86F ASP* 2.7 30.7 + - - +
88F ALA* 4.4 7.1 - - + +
89F VAL 3.2 5.6 - - - +
90F TYR* 3.0 51.0 + - + -
91F TYR* 5.2 0.2 - - - -
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLN* 2.8 41.5 + - - -
87E TYR* 3.7 7.5 + - - -
38F ARG* 1.3 77.6 - - - +
40F ALA* 1.3 67.6 + - - +
41F PRO* 3.7 1.4 - - - +
42F GLY 5.9 0.4 - - - +
43F LYS 3.5 19.0 + - - +
44F GLY 3.3 15.5 - - - +
45F LEU* 3.6 24.9 - - + +
88F ALA* 3.5 2.7 - - - -
89F VAL* 2.8 38.9 + - + +
91F TYR* 3.6 16.5 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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