Contacts of the strand formed by residues 75 - 80 (chain A) in PDB entry 3ZG2
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 GLN 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ILE 3.4 0.3 - - - +
71A SER* 3.7 2.2 - - - -
72A ILE 2.8 41.7 + - - +
73A GLY 3.1 3.5 - - - +
74A GLY* 1.3 77.9 - - - +
76A ARG* 1.3 94.3 + - - +
77A VAL* 3.3 8.0 + - + +
214A PHE* 4.9 13.7 - - + +
216A PRO* 5.9 3.1 - - - +
362A MET* 5.7 2.1 - - - +
377A GLY 3.9 19.0 + - - +
379A ILE* 3.7 32.4 - - + +
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Residues in contact with ARG 76 (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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30A LYS* 5.6 2.6 - - - +
31A THR* 3.1 37.3 + - - +
32A PRO* 4.5 1.0 + - - +
34A VAL* 3.8 27.2 - - + +
69A THR* 2.8 36.4 + - + +
70A ILE 3.7 4.5 - - - -
71A SER* 4.9 1.6 - - - +
74A GLY 3.9 4.6 + - - +
75A GLN* 1.3 84.1 + - - +
77A VAL* 1.3 59.7 + - - +
78A THR* 4.0 0.6 + - - -
375A PRO* 4.5 2.9 - - - +
378A ASP* 3.1 37.4 + - - +
379A ILE* 3.2 24.0 + - - +
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Residues in contact with VAL 77 (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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69A THR* 3.2 1.0 - - - +
70A ILE* 2.4 67.4 + - + +
72A ILE* 4.1 17.9 - - + -
75A GLN* 3.6 16.6 - - + +
76A ARG* 1.3 78.8 - - - +
78A THR* 1.3 60.0 + - - +
79A ILE* 3.7 5.7 + - + -
214A PHE* 4.5 14.8 - - + -
358A MET* 5.1 3.1 - - + -
360A MET* 5.9 0.7 - - + -
379A ILE* 3.3 26.0 - - + +
381A ALA* 4.4 17.3 - - + -
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Residues in contact with THR 78 (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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32A PRO* 3.9 22.5 - - + +
67A VAL* 4.1 12.1 - - + -
68A PHE 3.2 20.0 - - - +
69A THR* 2.6 23.4 + - - +
76A ARG* 4.0 1.1 + - - -
77A VAL* 1.3 70.5 - - - +
79A ILE* 1.3 57.8 + - - +
80A VAL* 5.6 1.1 - - + -
374A VAL* 4.9 12.3 - - + +
378A ASP* 3.6 15.3 + - - -
379A ILE 2.8 11.4 + - - +
380A ILE* 3.3 13.0 - - + +
381A ALA 2.7 32.3 + - - +
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Residues in contact with ILE 79 (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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48A PHE* 5.1 1.6 - - + -
55A PHE* 5.8 0.4 - - + -
56A MET* 3.8 21.1 - - + -
66A GLY 3.9 1.0 - - - +
67A VAL* 3.7 3.6 - - - +
68A PHE* 2.9 52.2 + - + -
70A ILE* 4.0 18.6 - - + -
77A VAL* 4.4 9.6 - - + +
78A THR* 1.3 75.0 - - - +
80A VAL* 1.3 67.7 + - - +
81A GLY 3.5 2.6 + - - -
358A MET* 3.7 28.5 - - + -
381A ALA* 3.5 7.0 - - + +
383A SER* 4.5 12.1 - - - +
386A LEU* 3.7 27.4 - - + -
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Residues in contact with VAL 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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67A VAL* 4.3 13.0 - - + -
78A THR* 5.2 2.2 - - + -
79A ILE* 1.3 71.2 - - - +
81A GLY* 1.3 59.9 + - - +
82A ASP 3.7 2.5 - - - +
85A GLU* 3.9 38.1 - - + +
86A HIS* 4.4 2.0 - - + +
89A PHE* 3.8 15.0 - - + +
369A VAL* 4.3 11.0 - - + -
380A ILE* 3.7 28.5 - - + -
381A ALA 2.7 23.1 + - - +
382A CYS* 3.5 29.3 - - - -
383A SER 4.0 5.2 + - - -
387A SER* 4.2 3.5 + - - -
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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