Contacts of the strand formed by residues 77 - 86 (chain A) in PDB entry 3ZO7
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 LEU 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A MET* 3.7 36.8 - - + -
8A THR 3.3 8.3 - - - +
9A VAL* 3.5 32.3 - - + -
71A LEU* 4.5 9.6 - - + -
73A PHE* 3.3 25.8 - - + +
74A PHE* 2.9 24.4 + - - +
75A PRO 3.5 0.7 - - - -
76A TYR* 1.3 79.3 - - - +
78A THR* 1.3 62.3 + - - +
79A ILE* 3.8 28.4 + - + +
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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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6A ARG* 3.5 4.7 - - - +
7A MET* 3.6 1.0 - - - -
8A THR* 2.9 44.3 + - - +
10A ASN* 3.9 11.7 + - - -
76A TYR 4.0 0.4 + - - -
77A LEU* 1.3 72.1 - - - +
79A ILE* 1.3 65.6 + - - +
80A ASP* 5.1 9.9 - - - +
49C LYS* 5.3 4.3 - - - +
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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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5A VAL* 4.0 14.6 - - + -
6A ARG 3.3 4.9 - - - +
7A MET* 4.6 4.7 - - + -
68A LEU* 4.4 18.6 - - + +
74A PHE* 3.8 26.7 - - + -
77A LEU* 3.8 29.5 + - + +
78A THR* 1.3 79.5 - - - +
80A ASP* 1.3 62.5 + - - +
81A VAL* 3.8 24.2 - - + -
48C GLY 3.6 25.8 - - - +
49C LYS* 2.6 39.2 + - + +
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Residues in contact with ASP 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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4A LEU 3.5 1.6 - - - +
5A VAL* 3.2 6.9 - - - +
6A ARG* 2.9 59.6 + - + +
78A THR* 5.1 10.6 - - - +
79A ILE* 1.3 79.2 - - - +
81A VAL* 1.3 62.1 + - - +
49C LYS* 4.2 9.7 + - - +
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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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3A TYR* 4.0 16.6 - - + -
4A LEU 3.6 2.2 - - - +
5A VAL* 4.3 5.6 - - + -
64A LEU* 3.8 22.0 - - + -
68A LEU* 4.0 17.0 - - + -
79A ILE* 3.8 20.3 + - + +
80A ASP* 1.3 78.6 - - - +
82A GLU* 1.3 67.6 + - - +
83A PRO* 4.6 1.3 - - - +
81B VAL 5.4 1.7 - - - +
83B PRO* 4.1 24.6 - - + +
47C THR* 4.0 21.1 - - + +
49C LYS* 5.4 4.5 - - - +
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Residues in contact with GLU 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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3A TYR* 3.5 2.3 - - - -
4A LEU* 2.8 61.9 + - + +
81A VAL* 1.3 79.7 - - - +
83A PRO* 1.3 77.3 - - + +
84A LEU* 4.7 1.6 - - + +
81B VAL 5.9 1.3 - - - +
6D ARG* 2.7 45.3 + - - -
46D THR* 4.2 11.3 - - - +
53D ILE* 4.2 3.6 - - - +
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Residues in contact with PRO 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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2A LEU 3.8 6.3 - - - +
3A TYR* 4.3 4.7 - - + -
82A GLU* 1.3 92.8 - - + +
84A LEU* 1.3 65.1 + - - +
3B TYR* 4.6 6.5 - - + -
61B HIS* 3.4 35.4 - - + +
81B VAL* 4.1 29.4 - - + +
83B PRO* 4.2 21.3 - - + -
46D THR* 4.8 0.9 - - - -
47D THR* 3.3 27.8 + - - +
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Residues in contact with LEU 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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1A MET* 5.5 0.2 - - - +
2A LEU* 2.9 34.2 + - + +
3A TYR 4.2 4.3 - - - -
4A LEU* 3.9 35.7 - - + +
55A VAL* 4.4 8.7 - - + -
82A GLU* 4.6 4.7 - - + +
83A PRO* 1.3 79.8 - - - +
85A SER* 1.3 61.2 + - - +
61B HIS* 3.2 21.3 - - - +
44D TRP* 3.8 44.6 - - + -
45D ARG 3.6 6.1 - - - +
46D THR* 5.2 0.9 - - - -
47D THR* 3.5 2.5 - - - -
53D ILE* 3.9 27.6 - - + -
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Residues in contact with SER 85 (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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2A LEU* 6.1 2.0 - - - -
84A LEU* 1.3 72.9 - - - +
86A HIS* 1.3 61.6 + - - +
87A HIS 3.4 0.3 + - - -
61B HIS* 3.4 17.2 + - - -
62B ASP* 3.2 12.6 - - - -
65B HIS* 3.8 9.1 - - - +
44D TRP* 3.6 9.8 - - - +
45D ARG* 2.7 52.0 + - - -
47D THR* 2.5 27.7 + - - +
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Residues in contact with HIS 86 (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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2A LEU* 6.5 0.2 - - - -
85A SER* 1.3 74.0 - - - +
87A HIS* 1.3 80.7 + - - +
88A PRO* 3.8 9.5 + - + +
90A ARG* 3.8 32.1 + - + +
92A GLY 5.3 6.7 - - - -
62B ASP* 2.7 26.2 + - - +
65B HIS* 5.9 1.7 - - - -
44D TRP* 5.5 3.8 - - - +
45D ARG* 3.7 7.5 - - - +
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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