Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 4ZGM
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 SER 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 2.7 43.6 + - - +
77A PRO 3.4 0.9 - - - -
78A GLY* 1.3 80.2 - - - +
80A PHE* 1.3 70.9 + - - +
81A VAL* 3.8 2.4 + - - +
103A PHE* 3.5 8.9 - - - -
104A CYS* 2.9 30.0 + - - +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 1.3 83.9 + - - +
81A VAL* 1.3 62.7 + - - +
82A ASN* 4.3 4.4 + - - +
101A TYR* 4.7 14.8 - + + -
102A ARG 3.4 14.4 - - - -
103A PHE* 3.6 28.7 - + + -
120A TRP* 3.9 28.7 - + - -
201A 32M 4.5 13.0 - - + -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TRP* 3.7 14.7 - - + -
73A PRO* 3.9 35.4 - - + -
74A ASP 4.7 0.7 - - - +
75A GLY* 3.7 22.4 - - - -
76A GLU 4.7 0.4 - - - +
79A SER* 4.2 10.8 - - - +
80A PHE* 1.3 78.3 - - - +
82A ASN* 1.3 64.1 + - - +
101A TYR* 3.3 6.9 - - - +
102A ARG 2.9 29.7 + - - +
104A CYS* 4.4 0.9 - - + -
110A TRP* 3.7 32.3 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 5.2 1.6 - - - +
80A PHE* 5.2 3.4 + - - +
81A VAL* 1.3 76.9 - - - +
83A VAL* 1.3 70.6 + - - +
99A HIS* 3.3 25.3 + - + -
100A VAL 3.3 4.9 - - - +
101A TYR* 3.6 29.0 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 5.1 2.2 - - - +
70A ALA* 4.1 12.3 - - + -
71A CYS 3.5 26.2 - - - +
72A TRP* 4.0 12.8 - - + -
73A PRO* 3.5 22.9 - - + -
82A ASN* 1.3 82.3 - - - +
84A SER* 1.3 65.2 + - - +
99A HIS* 3.2 7.6 - - - -
100A VAL* 2.8 53.2 + - + -
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 4.9 2.8 + - - -
83A VAL* 1.3 85.9 - - - +
85A CYS* 1.3 72.7 + - - +
86A PRO* 3.2 7.6 - - - +
96A PRO 5.9 2.2 - - - -
98A GLY 3.6 9.8 + - - -
99A HIS* 3.8 14.3 + - - -
100A VAL* 4.3 0.4 - - - +
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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