Contacts of the strand formed by residues 77 - 86 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B MET* 3.8 36.3 - - + -
8B THR 3.3 9.0 - - - +
9B VAL* 3.5 32.5 - - + -
52B ASN* 6.0 0.2 - - - +
71B LEU* 4.6 9.0 - - + -
73B PHE* 3.3 24.0 - - + +
74B PHE* 3.0 28.6 + - - +
75B PRO 3.5 0.9 - - - +
76B TYR* 1.3 78.3 - - - +
78B THR* 1.3 60.9 + - - +
79B ILE* 3.8 25.7 + - + +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.5 1.9 - - - +
7B MET* 3.5 4.9 - - - -
8B THR* 2.9 44.2 + - - +
10B ASN* 4.1 12.1 + - - -
76B TYR 4.1 0.2 + - - -
77B LEU* 1.3 73.0 + - - +
79B ILE* 1.3 65.9 + - - +
80B ASP* 4.9 9.1 - - - +
49D LYS* 5.1 6.3 - - - +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.0 14.8 - - + -
6B ARG 3.3 4.5 - - - +
7B MET* 4.7 4.0 - - + -
68B LEU* 4.3 16.8 - - + -
74B PHE* 3.7 26.0 - - + -
77B LEU* 3.8 30.2 + - + +
78B THR* 1.3 81.8 - - - +
80B ASP* 1.3 67.7 + - - +
81B VAL* 3.9 23.8 - - + -
48D GLY* 3.7 25.8 - - - +
49D LYS* 2.8 40.2 + - + +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU 3.5 1.4 - - - +
5B VAL* 3.3 8.8 - - - +
6B ARG* 3.0 55.7 + - + +
78B THR* 4.9 9.3 - - - +
79B ILE* 1.3 82.5 - - - +
81B VAL* 1.3 62.9 + - - +
82B GLU* 5.5 0.7 - - + -
49D LYS* 4.5 6.9 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 5.8 1.9 - - - +
83A PRO* 4.1 22.1 - - + +
3B TYR* 3.9 15.5 - - + -
4B LEU 3.7 2.5 - - - +
5B VAL* 4.5 4.5 - - + -
64B LEU* 3.8 23.8 - - + -
68B LEU* 4.0 16.8 - - + -
79B ILE* 3.9 19.7 + - + +
80B ASP* 1.3 78.6 - - - +
82B GLU* 1.3 66.8 + - - +
83B PRO* 4.4 2.9 - - - +
47D THR* 3.9 22.4 - - + +
48D GLY* 4.4 0.2 - - - -
49D LYS* 5.6 2.7 - - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 3.4 2.5 - - - -
4B LEU* 2.7 59.0 + - + +
80B ASP* 5.4 0.9 - - + +
81B VAL* 1.3 80.4 - - - +
83B PRO* 1.3 78.0 - - + +
84B LEU* 5.0 1.5 - - + +
6C ARG* 2.8 45.7 + - - -
46C THR* 3.7 17.5 - - - +
49C LYS* 6.0 1.0 - - - +
53C ILE* 4.3 2.3 - - - +
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Residues in contact with PRO 83 (chain B).
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* 4.8 2.9 - - + -
61A HIS* 3.6 34.1 - - + +
81A VAL* 4.1 28.0 - - + +
83A PRO* 4.2 23.3 - - + -
2B LEU 3.8 6.5 - - - +
3B TYR* 4.5 3.5 - - + -
81B VAL 4.4 0.7 - - - +
82B GLU* 1.3 93.5 - - + +
84B LEU* 1.3 64.8 + - - +
46C THR* 4.5 0.9 - - - -
47C THR* 3.3 31.6 + - + +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS* 3.2 21.8 - - - +
1B MET* 5.6 0.2 - - - +
2B LEU* 2.9 34.1 + - + +
3B TYR 4.4 0.2 - - - -
4B LEU* 3.9 36.1 - - + +
55B VAL* 4.4 12.3 - - + -
82B GLU* 4.4 2.7 - - - +
83B PRO* 1.3 81.9 - - - +
85B SER* 1.3 62.4 + - - +
44C TRP* 3.9 36.8 - - + -
45C ARG 3.5 10.3 - - - +
46C THR* 4.9 2.9 - - + -
47C THR* 3.5 2.2 - - - -
53C ILE* 4.1 28.7 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS* 3.3 21.7 + - - +
62A ASP* 3.0 15.6 + - - -
65A HIS* 3.8 10.4 - - - +
2B LEU* 6.0 2.2 - - - -
84B LEU* 1.3 71.4 - - - +
86B HIS* 1.3 60.7 + - - +
87B HIS 3.5 0.5 + - - -
94B ASP* 5.4 0.4 - - - -
44C TRP* 3.6 11.5 - - - +
45C ARG* 2.8 47.6 + - - -
47C THR* 2.8 22.8 + - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 2.7 26.6 + - - +
65A HIS* 5.6 2.8 - - - -
85B SER* 1.3 74.1 - - - +
87B HIS* 1.3 87.4 + - - +
88B PRO* 3.9 11.2 + - + +
90B ARG* 3.8 22.8 + - + +
92B GLY 5.2 4.3 - - - -
94B ASP* 3.3 31.9 + - - +
44C TRP* 5.5 0.2 - - - +
45C ARG* 3.8 7.3 - - - +
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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