Contacts of the strand formed by residues 82 - 90 (chain G) in PDB entry 3F5O
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 VAL 82 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G GLY* 1.3 80.2 - - - +
83G SER* 1.3 62.6 + - - +
84G VAL* 3.8 0.3 - - - +
136G LYS* 3.2 4.6 - - - -
137G HIS* 2.8 53.3 + - + +
149G UOC 3.8 12.1 - - + -
150G COA 3.7 46.9 - - + +
52H ILE* 4.3 14.6 - - + -
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Residues in contact with SER 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ASP* 3.6 12.5 + - - -
82G VAL* 1.3 71.6 - - - +
84G VAL* 1.3 59.4 + - - +
134G HIS* 2.7 35.5 + - - -
135G THR 3.9 1.8 - - - -
136G LYS* 3.6 4.5 - - - +
150G COA 3.2 47.6 + - - +
57H GLY* 5.3 0.2 - - - -
90H TYR* 3.3 29.5 - - - +
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Residues in contact with VAL 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 6.0 0.7 - - + -
85E ASP* 5.7 0.2 - - - +
113E LEU* 3.8 17.7 - - + -
115E PHE* 3.7 21.3 - - + -
135E THR* 4.0 10.1 - - + -
82G VAL 3.8 0.2 - - - +
83G SER* 1.3 76.2 - - - +
85G ASP* 1.3 77.1 + - + +
113G LEU* 4.6 3.1 - - + -
135G THR* 2.8 22.1 + - + +
136G LYS 4.0 2.0 - - - -
137G HIS* 3.5 39.9 - - + +
150G COA 4.1 5.6 - - + -
89H THR* 3.4 1.7 - - - +
90H TYR* 2.9 32.2 + - - -
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Residues in contact with ASP 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 3.7 36.3 - - + +
87E ASN* 4.8 7.1 + - - -
133E ARG* 4.7 1.2 + - - +
135E THR* 2.7 32.1 + - - +
84G VAL* 1.3 93.9 - - - +
86G MET* 1.3 60.3 + - - +
87G ASN* 6.0 1.3 - - - +
133G ARG 4.1 0.2 - - - +
134G HIS* 3.4 5.2 - - - -
135G THR* 2.8 30.7 + - - +
88H ILE 3.5 4.9 - - - +
89H THR* 2.7 26.4 + - - +
90H TYR* 4.7 1.3 - - - -
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Residues in contact with MET 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ALA* 3.8 32.8 - - + +
64G VAL* 3.8 25.8 - - + -
65G ASP* 4.1 16.2 - - + +
85G ASP* 1.3 75.8 - - - +
87G ASN* 1.3 73.1 + - - +
88G ILE* 4.1 4.3 - - + -
133G ARG 3.3 11.4 - - - +
134G HIS* 4.1 13.9 - - + -
57H GLY 4.6 2.2 - - - +
61H ALA* 4.2 2.9 - - + -
87H ASN* 3.3 3.3 - - - +
88H ILE* 2.8 50.8 + - + +
90H TYR* 3.5 30.4 - - + +
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Residues in contact with ASN 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 4.8 6.1 + - - -
87F ASN* 3.5 28.8 - - + +
89F THR* 4.8 2.4 + - - -
133F ARG* 2.8 36.0 + - - -
85G ASP* 6.0 1.2 - - - +
86G MET* 1.3 77.7 - - - +
88G ILE* 1.3 68.6 + - - +
132G GLY* 3.0 17.7 - - - -
133G ARG* 3.0 37.4 + - - +
86H MET 3.3 10.3 - - - +
87H ASN* 4.0 11.2 - - + -
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Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ARG* 4.2 1.1 - - - -
60G THR* 4.1 13.2 - - + -
61G ALA* 3.4 35.4 - - + -
64G VAL* 4.3 16.4 - - + -
86G MET* 4.1 14.4 - - + -
87G ASN* 1.3 81.2 - - - +
89G THR* 1.3 69.7 + - - +
90G TYR* 3.6 39.0 - - + +
130G ALA* 4.2 3.6 - - + -
131G GLN 3.5 11.4 - - - +
85H ASP* 3.5 4.0 - - - +
86H MET* 2.8 50.0 + - + +
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Residues in contact with THR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F PHE* 3.2 38.1 - - + -
133F ARG* 2.9 38.5 + - - +
135F THR* 4.0 3.2 + - - +
88G ILE* 1.3 71.2 - - - +
90G TYR* 1.3 63.3 + - - +
91G MET* 3.6 12.8 - - + +
130G ALA* 3.1 8.2 - - - +
131G GLN 2.9 31.7 + - - -
84H VAL 3.3 6.7 - - - +
85H ASP* 2.6 20.4 + - - +
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Residues in contact with TYR 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F PHE* 3.9 9.7 - - - -
57G GLY* 2.8 41.5 + - - -
60G THR* 3.7 20.4 - - + -
88G ILE* 3.6 41.0 - - + +
89G THR* 1.3 72.2 - - - +
91G MET* 1.3 61.1 + - - +
92G SER 5.9 0.2 - - - +
129G ILE* 3.9 5.6 - - + +
130G ALA* 4.3 7.4 - - + -
65H ASP* 4.9 0.7 + - - -
83H SER* 3.3 39.2 - - - +
84H VAL* 2.8 22.7 + - - +
86H MET* 3.7 20.2 - - + +
150H COA 3.2 42.0 + - + +
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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