Contacts of the strand formed by residues 37 - 42 (chain F) in PDB entry 4M75
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 LYS 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F SER* 1.3 85.4 + - - +
38F ILE* 1.3 63.2 + - - +
49F ILE* 4.5 20.0 - - + -
50F GLY* 4.3 5.8 - - - -
51F VAL* 3.8 33.6 - - + +
65F ASP 6.1 0.9 - - - -
67F VAL* 6.4 1.8 - - - -
104F SER* 3.4 12.0 + - - -
105F ALA* 3.9 14.6 + - + +
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Residues in contact with ILE 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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33F TYR* 4.5 22.7 - - + +
36F SER* 3.5 10.5 + - - +
37F LYS* 1.3 81.9 - - - +
39F ARG* 1.3 58.9 - - - +
40F VAL* 4.2 8.3 - - + -
48F VAL 3.8 0.7 - - - +
49F ILE* 3.2 28.4 - - - +
50F GLY 3.4 13.5 + - - +
52F LEU* 3.7 29.2 - - + -
61F LEU* 5.0 1.1 - - + -
63F LEU* 3.9 15.9 - - + -
102F LEU* 4.1 30.7 - - + -
103F SER 3.5 7.9 - - - +
104F SER* 4.0 8.7 - - - +
105F ALA 4.1 2.0 - - - +
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Residues in contact with ARG 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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38F ILE* 1.3 67.4 - - - +
40F VAL* 1.3 62.9 + - - +
41F LYS* 4.2 21.3 - - + +
47F LEU* 3.7 27.8 - - + +
48F VAL 3.9 1.6 - - - -
49F ILE* 4.3 14.6 - - + +
101F SER* 3.6 6.5 + - - +
102F LEU* 3.3 5.2 - - - -
103F SER* 2.2 74.6 + - - +
104F SER 4.5 8.1 + - - +
105F ALA* 4.7 5.8 - - + +
45G GLU* 2.6 33.7 + - - -
64G VAL* 4.6 12.6 - - - +
66G LEU* 3.5 16.1 - - - +
69G ILE* 4.5 4.9 - - - +
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Residues in contact with VAL 40 (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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38F ILE* 4.2 17.0 - - + -
39F ARG* 1.3 81.1 - - - +
41F LYS* 1.3 63.7 + - - +
42F LEU* 3.7 17.3 + - + +
47F LEU* 3.0 2.3 - - - -
48F VAL* 2.6 53.0 + - + +
61F LEU* 4.8 8.1 - - + -
63F LEU* 4.9 2.5 - - + -
94F ILE* 4.5 7.2 - - + -
99F LEU* 2.5 40.6 - - + -
101F SER 3.5 2.2 - - - +
102F LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 41 (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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39F ARG* 4.2 23.0 - - - +
40F VAL* 1.3 76.5 - - - +
42F LEU* 1.3 61.5 + - - +
46F LYS 5.4 0.7 - - - -
47F LEU* 3.6 37.4 - - + +
99F LEU 3.8 0.5 - - - -
100F VAL* 2.9 38.1 + - + +
101F SER* 3.1 27.0 + - - +
21G ASN* 5.6 1.8 - - - +
23G GLU* 3.0 38.4 + - - +
45G GLU* 3.9 8.4 + - - +
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Residues in contact with LEU 42 (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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79E ALA* 4.7 14.4 - - + -
80E ILE* 4.8 8.3 - - + -
40F VAL* 3.7 20.4 - - + +
41F LYS* 1.3 77.6 - - - +
43F MSE 1.3 69.2 + - - +
45F GLY* 3.3 14.6 + - - -
46F LYS* 2.9 32.2 + - + +
48F VAL* 3.8 22.9 - - + -
94F ILE* 3.2 34.5 - - + -
98F ILE* 3.5 24.2 - - + -
99F LEU* 4.1 7.2 - - - -
100F VAL* 4.4 5.3 - - - +
21G ASN* 5.9 0.7 + - - -
75G PHE* 5.7 1.3 - - - -
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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