Contacts of the strand formed by residues 132 - 136 (chain B) in PDB entry 1SXP
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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 5.0 0.2 - - + -
93B LYS* 5.0 1.3 - - - -
94B ILE* 3.4 26.5 - - + +
96B TYR* 3.9 18.6 - - + -
105B PHE* 3.2 51.1 - - + -
128B ILE* 4.6 5.6 - - + -
130B SER 3.7 7.4 - - - +
131B PRO* 1.3 80.3 - - - +
133B LYS* 1.3 70.0 + - - +
134B VAL* 4.5 2.7 - - + -
153B ASN* 2.7 23.9 + - - +
154B VAL* 3.2 16.7 - - + +
155B ILE* 2.8 33.4 + - - +
156B GLU 3.6 0.9 + - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS* 4.4 5.3 - - + +
94B ILE 2.9 10.7 + - - +
95B TYR* 3.6 19.7 - - + -
96B TYR* 2.9 26.7 + - - +
131B PRO 4.4 0.2 + - - -
132B ILE* 1.3 74.6 - - - +
134B VAL* 1.3 67.1 + - - +
135B ILE* 3.6 14.9 + - + -
156B GLU* 3.3 51.9 + - + +
158B GLU* 2.7 36.8 + - - -
347B LYS 4.4 1.8 + - - -
348B ALA* 2.8 31.6 + - - +
350B ASP* 4.3 9.7 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 3.6 9.2 - - + +
98B PHE* 3.5 35.7 - - + -
132B ILE* 4.5 7.9 - - + -
133B LYS* 1.3 76.5 - - - +
135B ILE* 1.3 63.5 + - - +
136B SER* 3.5 4.6 + - - +
144B ALA* 4.9 0.4 - - + -
148B HIS* 3.8 22.2 - - + +
154B VAL* 3.6 26.0 - - + -
156B GLU 2.7 9.3 + - - -
157B PHE* 3.4 24.5 - - + -
158B GLU* 2.9 27.5 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 4.8 10.8 - - + -
96B TYR 2.9 9.4 + - - +
97B LEU* 3.8 23.3 - - + -
98B PHE 2.9 25.1 + - - -
133B LYS* 3.6 37.5 - - + +
134B VAL* 1.3 71.8 - - - +
136B SER* 1.3 60.2 + - - +
158B GLU* 3.3 7.4 - - + +
160B PHE* 3.4 35.2 - - + -
162B ILE* 3.7 16.4 - - + +
345B PHE* 5.6 2.5 - - + -
348B ALA* 3.6 26.5 - - + +
349B ILE* 5.3 2.9 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.8 16.2 - - - -
134B VAL* 3.5 5.0 + - - -
135B ILE* 1.3 73.1 - - - +
137B GLN* 1.3 60.6 + - - +
138B GLY* 2.8 24.1 + - - -
140B ASN 4.9 0.5 + - - -
141B LEU* 3.7 24.5 - - - +
144B ALA* 4.1 19.0 - - - +
157B PHE* 5.9 0.2 - - - -
158B GLU 2.6 9.7 + - - -
159B TYR* 3.3 5.0 - - - -
160B PHE 2.8 28.6 + - - -
265B PHE* 5.0 1.0 - - - -
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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