Contacts of the strand formed by residues 76 - 81 (chain G) in PDB entry 4M7A
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 76 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.3 29.3 + - + +
59A SER* 4.5 0.3 + - - -
17G ILE* 3.7 24.5 - - + -
18G GLU 3.6 4.5 - - - -
19G LEU* 4.3 0.9 - - + -
20G LYS* 4.2 11.7 - - - -
36G MET* 3.5 34.8 - - + +
38G LEU* 3.9 20.2 - - + -
71G ILE* 3.7 20.9 - - + -
72G ARG 3.8 2.5 - - - +
73G GLY* 3.3 18.1 + - - +
74G THR 4.6 1.2 - - - +
75G PHE* 1.3 79.7 - - - +
77G LYS* 1.3 60.9 + - - +
78G PHE 3.8 11.7 - - - +
79G ILE* 3.8 15.0 - - + -
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Residues in contact with LYS 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 6.3 0.4 - - + -
19A ASP* 4.9 7.0 - - - +
56A LEU* 3.3 5.9 - - - +
57A ARG* 3.1 27.9 + - - +
60A GLU* 3.3 38.6 - - - +
18G GLU* 2.9 47.5 + - + +
19G LEU 3.5 18.7 + - - +
20G LYS* 4.0 21.6 + - + +
22G GLY* 4.6 7.3 - - - -
75G PHE 3.9 1.4 + - - -
76G ILE* 1.3 74.1 - - - +
78G PHE* 1.3 73.2 - - + +
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Residues in contact with PHE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.7 8.7 - - + -
21A GLU* 5.9 2.2 - - - -
50A ILE* 5.5 3.4 - - + -
54A GLN* 4.0 24.7 - - - +
55A LEU 3.1 13.9 - - - +
56A LEU* 3.7 17.0 - - + +
57A ARG* 5.2 0.2 - - - -
60A GLU* 5.6 0.7 - - - -
16G GLN 4.0 0.8 - - - +
17G ILE* 3.7 0.9 - - - -
18G GLU* 2.9 69.1 + - + +
76G ILE* 3.8 2.9 - - - +
77G LYS* 1.3 97.9 - - + +
79G ILE* 1.3 66.6 + - - +
80G LYS* 4.2 28.5 - - + -
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Residues in contact with ILE 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.3 5.8 - - - -
55A LEU* 2.6 55.2 + - + +
7G LEU* 4.1 27.1 - - + -
15G MET* 4.1 7.0 - - - -
16G GLN 3.7 2.5 - - - +
17G ILE* 3.7 31.0 - - + -
36G MET* 5.0 2.7 - - - -
38G LEU* 4.1 12.6 - - + -
76G ILE* 3.8 20.9 - - + -
78G PHE* 1.3 77.9 - - - +
80G LYS* 1.3 66.7 + - - +
81G LEU* 3.5 24.1 + - + +
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Residues in contact with LYS 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.3 41.5 + - - +
51A SER* 4.4 11.4 - - - +
53A ALA 4.2 3.1 - - - -
54A GLN* 4.0 13.0 - - - +
15G MET* 3.4 8.1 - - - +
16G GLN* 2.9 74.8 + - + +
78G PHE* 4.2 22.4 - - + -
79G ILE* 1.3 70.5 - - - +
81G LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.3 12.3 - - + -
51A SER* 3.9 7.3 + - - -
53A ALA* 3.1 26.3 + - + +
54A GLN 4.4 4.5 - - - +
55A LEU* 4.5 11.7 - - + +
6G LEU* 4.1 21.3 - - + -
7G LEU* 4.4 9.6 - - + -
15G MET* 3.9 24.7 - - + -
79G ILE* 3.7 28.7 - - + +
80G LYS* 1.3 76.0 - - - +
82G GLN* 1.3 71.5 + - - +
83G ASP* 3.7 6.2 + - - +
85G ILE* 4.0 25.6 - - + -
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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