Contacts of the strand formed by residues 91 - 96 (chain O) in PDB entry 2AXT
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77O LEU* 3.6 33.0 - - + +
79O LYS* 3.5 37.0 - - + +
89O ALA 5.2 2.9 - - - -
90O GLU* 1.3 78.9 - - - +
92O VAL* 1.3 62.8 + - - +
93O PRO* 4.2 1.6 - - - +
244O GLU* 3.5 28.0 - - - -
258O GLU* 4.3 10.8 - - + -
259O VAL 4.2 11.0 - - - -
260O LYS* 3.7 48.5 - - + +
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Residues in contact with VAL 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O LEU* 3.1 6.9 - - - -
78O VAL 2.9 30.5 + - - +
80O GLU* 4.5 15.7 - - + -
90O GLU* 3.6 15.8 + - + +
91O PHE* 1.3 76.3 - - - +
93O PRO* 1.3 94.9 - - + +
94O THR* 3.9 2.1 - - + +
136O MET* 6.1 5.2 - - + -
137O ALA* 4.6 13.7 - - + -
5084b THR* 3.8 30.1 - - + -
5085b GLY 4.9 0.2 - - - +
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Residues in contact with PRO 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O THR* 5.6 5.8 - - + -
76O PHE 3.9 7.0 - - - +
77O LEU* 4.5 7.4 - - + -
91O PHE 4.5 2.2 - - - +
92O VAL* 1.3 106.2 - - + +
94O THR* 1.3 61.7 + - - +
136O MET* 5.0 0.2 - - - +
137O ALA* 4.6 9.0 + - - +
5084b THR* 4.0 18.6 - - + +
5085b GLY* 4.6 11.7 + - - +
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Residues in contact with THR 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O PHE* 3.2 24.1 + - - +
78O VAL* 3.8 21.3 - - + -
92O VAL 3.9 7.0 - - - +
93O PRO* 1.3 81.7 - - - +
95O LYS* 1.3 61.6 + - - +
96O LEU 3.9 1.2 + - - -
134O VAL* 3.4 25.2 - - + +
135O GLN 3.6 9.9 - - - -
136O MET* 3.5 28.5 - - + +
137O ALA 5.1 1.3 - - - +
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Residues in contact with LYS 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 5.2 10.8 - - - +
103A ASP* 5.3 10.5 - - + +
94O THR* 1.3 72.2 - - - +
96O LEU* 1.3 60.0 + - - +
97O VAL 3.2 1.7 + - - -
134O VAL* 3.2 4.1 - - - -
135O GLN* 2.7 50.7 + - + +
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Residues in contact with LEU 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 5.3 3.5 - - - +
101A SER* 4.8 4.7 + - - -
104A GLU* 4.3 9.9 - - - +
76O PHE* 5.1 10.8 - - + -
94O THR 3.9 2.4 + - - -
95O LYS* 1.3 68.8 - - - +
97O VAL* 1.3 61.2 + - - +
98O THR* 3.4 27.3 - - - +
99O ARG 3.1 25.4 - - - +
100O GLU* 5.3 1.3 - - + -
102O THR* 4.1 14.8 - - + -
132O VAL* 3.9 22.2 - - + -
133O THR 3.6 9.6 - - - +
134O VAL* 4.1 9.4 - - + +
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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