Contacts of the strand formed by residues 91 - 96 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.9 29.8 - - + -
31B PHE* 3.4 42.0 - + + -
33B ASN 3.8 2.6 - - - +
34B ALA* 3.2 30.2 - - + -
35B LEU* 3.0 25.3 + - - +
55B LEU* 4.9 0.4 - - + -
60B ILE* 3.9 13.7 - - + -
89B SER* 3.5 2.4 - - - -
90B ASP* 1.3 104.3 + - - +
92B VAL* 1.3 69.3 + - - +
93B ILE* 3.6 28.3 - - + -
131B LEU* 4.1 5.6 - - - +
132B PRO* 3.5 17.3 - - + +
133B LEU 5.8 0.2 - - - -
134B MET* 5.1 6.7 - - + -
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Residues in contact with VAL 92 (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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35B LEU* 3.5 25.6 - - + +
37B VAL* 4.0 11.0 - - + -
84B LEU* 4.5 2.9 - - + -
91B PHE* 1.3 80.3 - - - +
93B ILE* 1.3 67.4 + - - +
104B ALA* 3.8 21.5 - - + +
107B ILE* 4.8 1.1 - - + -
108B ALA* 4.1 20.4 - - + +
131B LEU* 3.8 20.4 - - + -
132B PRO 2.8 13.0 + - - +
133B LEU* 3.2 25.0 - - + -
134B MET 2.8 24.4 + - - -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.9 0.2 - - + -
26B LEU* 5.0 0.2 - - + -
34B ALA* 4.0 6.1 - - + -
35B LEU 2.9 11.0 + - - +
36B ILE* 3.3 12.6 - - + +
37B VAL 2.8 25.1 + - - -
51B VAL* 4.7 9.2 - - + -
55B LEU* 3.7 35.0 - - + -
91B PHE* 3.6 30.1 - - + -
92B VAL* 1.3 81.6 - - - +
94B SER* 1.3 63.9 + - - +
95B LEU* 3.8 1.3 + - + -
134B MET* 3.1 23.3 - - + +
136B ILE* 3.7 29.2 - - + -
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Residues in contact with SER 94 (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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37B VAL* 3.4 4.9 - - - -
93B ILE* 1.3 74.7 - - - +
95B LEU* 1.3 57.5 + - - +
100B PRO 3.8 2.9 - - - -
101B HIS* 2.7 37.0 + - - -
104B ALA* 3.5 27.6 - - - -
133B LEU* 4.0 2.2 - - - +
134B MET 2.9 6.9 + - - -
135B SER* 2.8 21.3 + - - -
136B ILE* 2.8 34.2 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.4 11.4 - - + -
37B VAL 2.9 11.2 + - - +
38B SER* 2.7 38.1 + - - +
42B MET* 3.8 3.7 - - + +
47B VAL* 3.7 24.9 - - + -
48B VAL* 3.8 33.9 - - + -
51B VAL* 3.7 27.4 - - + -
93B ILE* 5.1 3.4 - - + -
94B SER* 1.3 76.4 - - - +
96B GLY* 1.3 62.2 + - - +
100B PRO* 3.6 6.8 - - - +
136B ILE* 3.4 21.8 - - + -
138B THR* 3.9 14.6 - - + -
179B LEU* 4.4 1.3 - - + -
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Residues in contact with GLY 96 (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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39B ASP* 5.3 0.4 - - - -
42B MET* 4.1 10.5 - - - -
95B LEU* 1.3 78.4 - - - +
97B GLY* 1.3 62.4 - - - -
100B PRO* 4.0 5.2 - - - -
101B HIS* 3.2 12.8 + - - -
136B ILE 3.1 6.5 + - - -
138B THR* 2.9 41.3 + - - +
1385B NAD 4.8 1.8 - - - -
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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