Contacts of the strand formed by residues 94 - 98 (chain B) in PDB entry 1SXQ
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 ILE 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.7 10.3 - - + +
64B VAL* 3.6 30.1 - - + -
87B MET* 3.7 41.3 - - + +
90B TYR* 3.9 11.0 - - + -
92B SER 3.8 8.1 - - - +
93B LYS* 1.3 77.3 - - - +
95B TYR* 1.3 67.0 + - - +
96B TYR* 4.7 2.0 - - + +
128B ILE* 3.9 21.3 - - + -
130B SER* 4.0 11.9 - - - -
131B PRO 3.0 8.9 + - - +
132B ILE* 3.4 15.9 - - + +
133B LYS* 2.8 27.2 + - - +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 3.5 28.2 + - + -
62B LEU 2.9 23.6 + - - +
63B ILE* 3.3 9.9 - - + +
64B VAL 2.8 31.4 + - - -
93B LYS* 3.3 37.4 - - + +
94B ILE* 1.3 72.9 - - - +
96B TYR* 1.3 56.3 + - - +
97B LEU 3.7 0.9 + - - -
133B LYS* 3.5 19.3 - - + -
135B ILE* 4.1 15.9 - - + -
348B ALA 3.6 14.8 - - - -
349B ILE* 3.6 31.8 + - + -
350B ASP* 2.5 38.1 + - - +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 3.5 34.0 - - + +
64B VAL* 3.5 20.4 - - + +
66B ASN* 3.2 29.4 - - + +
67B SER 3.5 1.9 + - - -
87B MET* 5.0 2.9 - - + -
94B ILE* 3.8 2.3 + - + -
95B TYR* 1.3 70.0 - - - +
97B LEU* 1.3 63.8 + - - +
98B PHE* 3.2 11.3 + + + -
103B LEU 2.7 24.8 + - - -
104B PRO* 3.4 2.8 + - + -
105B PHE* 3.2 45.1 + + + -
132B ILE* 3.9 19.7 - - + -
133B LYS 2.9 10.3 + - - +
134B VAL* 3.6 7.9 - - + -
135B ILE 2.9 26.9 + - - -
148B HIS* 4.1 10.5 - - - -
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Residues in contact with LEU 97 (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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5B ILE* 4.5 2.5 - - + -
26B LEU* 3.8 35.9 - - + -
30B ILE* 5.9 0.4 - - + -
63B ILE* 3.5 32.1 - - + -
64B VAL 2.8 14.5 + - - +
65B VAL* 4.2 10.8 - - + -
66B ASN* 3.1 31.6 + - - +
95B TYR 4.7 0.7 - - - +
96B TYR* 1.3 68.9 - - - +
98B PHE* 1.3 60.2 + - - +
99B THR* 3.4 6.5 + - + +
135B ILE* 3.9 34.8 - - + -
162B ILE* 4.0 17.9 - - + -
345B PHE* 4.6 14.4 - - + -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 3.4 5.8 - - - -
96B TYR* 3.2 6.4 + + + +
97B LEU* 1.3 69.3 - - - +
99B THR* 1.3 59.6 + - - +
100B ASP 3.1 22.9 - - - -
101B ILE* 3.6 41.5 - - + -
103B LEU 3.8 6.5 - - - -
104B PRO* 3.5 22.2 - - + -
134B VAL* 3.7 19.1 - - + -
135B ILE 2.9 16.3 + - - +
136B SER* 4.2 7.2 - - - -
137B GLN* 3.1 24.9 + - - +
144B ALA* 4.1 22.0 - - + -
147B ALA* 3.9 11.9 - - + -
148B HIS* 4.0 20.0 - + - -
162B ILE* 4.2 0.2 - - - +
265B PHE* 4.2 8.1 - + - -
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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
------------------------------------------------------------
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