Contacts of the strand formed by residues 77 - 82 (chain g) in PDB entry 5OA3
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 PHE 77 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71g ILE* 4.2 4.0 - - - +
72g SER* 3.1 41.1 + - - +
74g ASP* 4.2 5.0 + - + +
76g GLN* 1.3 102.9 - - + +
78g ALA* 1.3 60.1 + - - +
89g LEU* 3.8 31.2 - - + -
90g TRP 3.3 14.4 - - - -
91g ASP* 3.9 20.0 - - - -
92g LEU* 4.9 1.6 - - - +
98g THR* 4.1 18.6 - - + -
113g PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 78 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32g LEU* 3.7 29.6 - - + -
40g ILE* 6.1 1.1 - - + -
59g LEU* 5.9 0.2 - - + -
69g VAL* 5.1 1.1 - - + -
70g VAL 3.9 9.0 - - - +
71g ILE* 4.5 2.5 - - + +
72g SER* 4.9 0.7 - - - +
77g PHE* 1.3 74.5 - - - +
79g LEU* 1.3 62.6 + - - +
89g LEU* 3.3 11.8 - - - +
90g TRP* 2.9 44.5 + - + -
92g LEU* 4.1 11.0 - - + -
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Residues in contact with LEU 79 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68g ASP 4.0 0.5 - - - +
69g VAL* 3.6 9.9 - - - +
70g VAL* 3.2 40.8 + - + +
78g ALA* 1.3 77.3 - - - +
80g SER* 1.3 61.7 + - - +
87g LEU* 4.1 5.6 - - + -
88g ARG 3.3 22.2 - - - +
89g LEU* 3.8 17.7 - - + -
90g TRP* 4.8 1.1 - - - -
101g PHE* 3.8 15.3 - - + -
111g VAL* 3.5 30.4 - - + +
113g PHE* 4.2 18.4 - - + -
120g ILE* 3.6 32.1 - - + -
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Residues in contact with SER 80 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40g ILE* 3.5 27.6 - - - -
62g HIS* 3.0 16.5 + - - -
66g VAL* 3.8 8.3 - - - -
68g ASP 3.8 4.0 - - - -
69g VAL* 5.1 0.7 - - - -
79g LEU* 1.3 75.5 - - - +
81g GLY* 1.3 61.4 + - - +
86g THR 3.6 1.4 - - - +
87g LEU* 3.3 7.7 - - - -
88g ARG* 2.9 31.7 + - - +
90g TRP* 2.7 26.4 + - - -
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Residues in contact with GLY 81 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66g VAL* 3.3 9.7 - - - +
67g SER* 2.9 33.2 + - - -
68g ASP 3.3 9.7 + - - -
80g SER* 1.3 71.7 - - - +
82g SER* 1.3 60.3 + - - -
86g THR 3.7 1.6 - - - -
87g LEU* 3.5 22.0 - - - +
108g VAL* 3.9 9.0 - - - -
110g SER 6.1 0.2 - - - -
111g VAL* 4.1 5.0 - - - +
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Residues in contact with SER 82 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62g HIS* 3.3 29.9 - - - +
64g HIS 3.4 16.1 + - - -
65g PHE 2.6 21.3 + - - -
67g SER* 4.3 1.8 - - - +
81g GLY* 1.3 75.5 - - - -
83g TRP* 1.3 52.9 + - - +
84g ASP* 2.9 19.1 + - - -
85g GLY* 2.7 27.9 + - - -
86g THR 2.9 14.9 + - - -
108g VAL* 3.6 9.5 + - - +
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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