Contacts of the strand formed by residues 91 - 96 (chain C) in PDB entry 3OX4
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 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.7 29.6 - - + -
31C PHE* 3.3 43.1 - + + -
33C ASN 3.8 0.3 - - - +
34C ALA* 3.1 30.7 - - + -
35C LEU* 3.0 23.4 + - - +
55C LEU* 4.5 0.4 - - + -
60C ILE* 3.8 14.4 - - + -
89C SER* 3.6 1.9 - - - -
90C ASP* 1.3 85.3 + - - +
92C VAL* 1.3 72.9 + - - +
93C ILE* 3.4 26.9 - - + -
131C LEU* 3.9 5.5 - - - +
132C PRO* 3.5 25.8 - - + +
133C LEU 5.7 0.2 - - - -
134C MET* 5.0 7.4 - - + -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.6 15.7 - - + +
37C VAL* 3.9 11.2 - - + -
84C LEU* 4.0 26.5 - - + -
91C PHE* 1.3 79.1 - - - +
93C ILE* 1.3 65.6 + - - +
104C ALA* 3.8 21.5 - - + +
107C ILE* 4.8 0.9 - - + -
108C ALA* 4.2 20.4 - - + +
131C LEU* 4.2 6.3 - - + -
132C PRO 2.9 10.7 + - - +
133C LEU* 3.4 21.6 - - + -
134C MET 2.8 31.5 + - - -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 5.9 0.4 - - + -
34C ALA* 3.9 7.2 - - + -
35C LEU 2.9 11.7 + - - +
36C ILE* 3.4 10.3 - - + +
37C VAL 2.9 23.9 + - - +
51C VAL* 4.6 15.3 - - + -
55C LEU* 3.6 36.1 - - + -
91C PHE* 3.4 35.7 - - + -
92C VAL* 1.3 74.1 - - - +
94C SER* 1.3 71.6 + - - +
95C LEU* 3.8 3.9 + - + -
134C MET* 3.2 21.5 - - + +
136C ILE* 4.0 17.3 - - + -
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL 3.4 6.7 - - - -
92C VAL 4.2 0.4 - - - -
93C ILE* 1.3 74.3 - - - +
95C LEU* 1.3 59.3 + - - +
100C PRO 3.8 2.5 - - - -
101C HIS* 2.5 39.9 + - - -
104C ALA* 3.5 26.5 - - - -
133C LEU* 4.4 1.6 - - - +
134C MET 2.9 7.5 + - - -
135C SER* 3.0 19.6 + - - -
136C ILE* 2.9 30.7 + - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.5 12.3 - - + -
37C VAL 2.9 9.6 + - - +
38C SER* 2.6 39.8 + - - +
39C ASP 4.2 0.2 + - - -
42C MET* 3.7 3.5 - - + +
47C VAL* 3.7 29.2 - - + -
48C VAL* 3.7 40.6 - - + +
51C VAL* 3.9 15.9 - - + -
93C ILE* 4.7 2.7 - - + +
94C SER* 1.3 76.8 - - - +
96C GLY* 1.3 61.4 + - - +
100C PRO* 3.8 6.2 - - - +
136C ILE* 3.5 29.8 - - + -
138C THR* 4.2 7.0 - - + -
179C LEU* 4.2 2.0 - - + -
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Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASP* 4.9 1.6 - - - -
42C MET* 4.0 9.6 - - - -
95C LEU* 1.3 73.7 - - - +
97C GLY* 1.3 62.3 + - - -
100C PRO* 3.9 3.1 - - - +
101C HIS* 3.2 11.8 + - - -
136C ILE 3.1 8.3 + - - +
137C ASN* 3.5 0.2 - - - +
138C THR* 2.8 49.1 + - - +
1385C NAD 4.8 1.1 - - - -
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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