Contacts of the strand formed by residues 78 - 86 (chain B) in PDB entry 5ZF6
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 THR 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLN* 3.2 2.9 - - - +
75B SER 2.9 35.3 + - - -
77B ASP* 1.3 78.2 - - - +
79B ALA* 1.3 59.6 + - - +
80B VAL* 4.8 1.1 - - + -
158B ALA 3.3 15.3 - - - +
159B VAL* 3.5 4.3 - - + -
160B ASP* 2.8 36.4 + - - -
163B ASN* 3.1 22.2 + - - +
165B PRO* 3.8 19.1 - - + -
168B LEU* 3.5 18.2 - - + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.4 11.7 - - + -
73B VAL 3.3 5.6 - - - +
74B GLN* 3.7 28.3 - - + +
77B ASP 4.1 1.0 + - - -
78B THR* 1.3 74.6 - - - +
80B VAL* 1.3 64.6 + - - +
156B LEU* 3.9 0.3 - - - -
157B LEU* 2.9 35.1 + - + -
158B ALA* 3.2 18.1 + - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 3.9 0.2 - - - +
72B VAL* 3.2 5.7 - - - +
73B VAL* 2.9 31.9 + - - +
78B THR* 4.8 0.4 - - + -
79B ALA* 1.3 78.7 - - - +
81B MET* 1.3 67.3 + - - +
82B VAL* 4.2 15.8 + - + +
154B CYS* 4.3 9.6 - - + -
155B ASN 3.7 13.7 - - - +
156B LEU* 3.7 17.7 - - + -
157B LEU* 4.4 2.2 - - - +
165B PRO* 3.7 38.1 - - + +
168B LEU* 3.9 17.3 - - + +
169B ALA* 4.4 9.9 - - + +
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 5.9 2.0 - - + -
61B GLY* 5.9 4.9 - - - -
70B SER* 5.3 4.5 - - - -
71B ALA 3.3 12.8 - - - +
72B VAL* 3.8 16.6 - - + -
80B VAL* 1.3 71.7 - - - +
82B VAL* 1.3 67.0 + - - +
83B THR* 4.6 17.2 - - + +
153B LEU* 3.8 1.5 - - + +
154B CYS* 3.4 1.2 - - - -
155B ASN* 2.6 74.2 + - + +
157B LEU* 3.9 17.6 - - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER* 3.4 3.3 - - - -
71B ALA 2.9 31.5 + - - +
80B VAL* 4.2 11.9 - - + +
81B MET* 1.3 79.2 - - - +
83B THR* 1.3 66.5 + - - +
152B VAL* 3.7 18.8 - - + -
153B LEU 3.2 10.3 - - - +
154B CYS* 3.8 17.9 - - + -
169B ALA* 3.9 6.5 - - - +
172B GLY* 3.5 33.7 - - - +
173B ALA* 3.7 23.1 - - - +
176B ALA* 3.7 5.2 - - + +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.2 18.6 - - + -
69B GLY 3.4 6.3 - - - -
70B SER* 4.0 17.0 - - - -
81B MET* 4.6 19.3 - - + +
82B VAL* 1.3 80.4 - - - +
84B ALA* 1.3 60.9 + - - +
85B VAL* 5.0 5.0 - - - +
151B GLN 3.6 1.6 - - - +
152B VAL* 3.3 4.5 - - - +
153B LEU* 2.9 53.0 + - + +
176B ALA* 4.4 1.3 - - - -
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Residues in contact with ALA 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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68B ASP* 3.0 24.6 + - - +
69B GLY 2.9 14.6 + - - +
83B THR* 1.3 74.4 - - - +
85B VAL* 1.3 62.7 + - - +
150B THR* 5.6 0.4 - - + -
151B GLN 3.4 6.5 - - - +
152B VAL* 4.4 8.3 - - + -
176B ALA* 4.1 15.2 - - + +
177B LEU* 4.0 34.8 - - + +
180B SER* 4.8 0.2 - - - -
182B ILE* 3.8 6.5 - - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 6.3 2.9 - - + -
67B ALA* 3.6 26.7 - - + +
68B ASP* 3.7 19.3 - - - +
83B THR* 5.0 4.9 - - - +
84B ALA* 1.3 81.9 - - - +
86B SER* 1.3 68.3 + - - +
87B LYS* 6.0 2.2 - - + -
149B ASP 4.5 0.4 - - - -
150B THR* 3.1 8.7 - - - +
151B GLN* 2.9 43.9 + - + +
182B ILE* 3.9 2.7 - - - -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 3.0 10.6 + - - +
85B VAL* 1.3 81.9 - - - +
87B LYS* 1.3 60.8 + - - +
88B THR* 3.8 0.9 + - - +
146B TYR* 3.0 18.6 + - - -
148B TYR* 3.6 10.4 - - - +
149B ASP 3.1 8.0 + - - -
150B THR* 3.1 20.6 + - - -
151B GLN* 5.5 0.2 - - - -
182B ILE* 3.4 24.2 - - - -
271B ARG* 3.0 24.5 + - - -
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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
------------------------------------------------------------
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