Contacts of the strand formed by residues 76 - 80 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H ARG* 3.8 25.9 + - + +
59H SER* 4.4 0.5 + - - -
17N ILE* 4.1 11.2 - - + -
18N GLU 3.7 4.9 - - - +
19N LEU* 4.4 0.4 - - + +
20N LYS* 3.8 12.5 - - - -
36N MET* 3.9 26.2 - - + +
38N LEU* 4.1 20.2 - - + -
71N ILE* 4.4 8.3 - - + -
72N ARG 4.1 6.5 - - - +
73N GLY* 3.1 18.7 + - - +
74N THR 4.8 1.0 - - - -
75N PHE* 1.3 80.6 - - - +
77N LYS* 1.3 77.6 + - - +
78N PHE 3.7 14.1 - - - +
79N ILE* 3.9 21.1 - - + -
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Residues in contact with LYS 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ASP* 5.1 3.8 - - - +
56H LEU* 4.3 3.5 - - + +
57H ARG* 3.1 33.3 + - - +
60H GLU* 3.3 40.0 - - + +
18N GLU* 2.8 38.5 + - + +
19N LEU 4.2 2.2 + - - -
20N LYS* 3.4 47.6 + - + +
21N ASN 4.2 1.2 - - - +
22N GLY* 4.5 7.1 - - - +
76N ILE* 1.3 70.6 - - - +
78N PHE* 1.3 70.7 + - + +
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Residues in contact with PHE 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H LEU* 6.5 0.9 - - + -
50H ILE* 5.9 1.8 - - + -
54H GLN* 4.2 14.6 - - - +
55H LEU 2.9 18.8 - - - +
56H LEU* 3.7 24.9 - - + -
16N GLN* 5.0 1.8 - - - -
18N GLU* 2.6 72.6 + - + +
76N ILE* 3.7 3.5 - - - +
77N LYS* 1.3 90.5 - - + +
79N ILE* 1.3 67.3 + - - +
80N LYS* 3.7 39.5 - - + -
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Residues in contact with ILE 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLN* 3.7 1.2 - - - -
55H LEU* 2.7 52.6 + - + +
57H ARG* 6.4 0.2 - - - -
7N LEU* 4.3 26.9 - - + -
15N MET* 4.6 4.9 - - + -
16N GLN 3.5 5.4 - - - +
17N ILE* 3.6 29.6 - - + -
36N MET* 4.8 5.6 - - - -
38N LEU* 4.6 3.6 - - + -
76N ILE* 3.9 28.3 - - + -
78N PHE* 1.3 81.6 - - - +
80N LYS* 1.3 60.4 + - - +
81N LEU* 3.5 27.2 + - + +
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Residues in contact with LYS 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 3.2 43.1 + - + +
51H SER* 4.6 7.4 - - - -
53H ALA 4.7 0.2 - - - -
54H GLN* 3.8 20.0 - - - +
16N GLN* 2.9 65.6 + - + +
18N GLU* 5.2 1.3 + - - -
78N PHE* 3.7 28.5 + - + -
79N ILE* 1.3 69.8 - - - +
81N LEU* 1.3 66.7 + - - +
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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