Contacts of the strand formed by residues 130 - 138 (chain B) in PDB entry 2OSL
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 SER 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LEU* 5.6 2.1 - - - +
149A LEU* 3.6 20.0 - - - +
151A LYS* 4.0 11.8 - - - -
118B PRO 4.3 1.2 - - - +
119B PRO* 3.5 20.7 - - - +
123B GLN* 2.8 30.4 + - - +
127B GLY 4.7 0.9 + - - -
129B ALA* 1.3 71.8 - - - +
131B VAL* 1.3 63.3 + - - +
132B VAL* 4.0 7.5 + - - +
177B THR* 5.0 6.1 + - - -
178B LEU 3.6 5.4 - - - -
179B THR* 3.5 17.5 + - - +
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Residues in contact with VAL 131 (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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116B ILE* 4.2 2.2 - - + -
117B PHE 3.5 14.6 - - - +
119B PRO* 4.0 15.5 - - + -
129B ALA 5.2 1.6 - - - +
130B SER* 1.3 75.2 - - - +
132B VAL* 1.3 62.5 + - - +
147B TRP* 3.5 29.6 - - + -
177B THR* 3.3 2.9 - - - -
178B LEU* 2.7 54.4 + - + +
180B LEU* 4.7 6.5 - - + -
185B TYR* 4.5 13.0 - - + -
191B TYR* 4.6 9.6 - - + -
208B PHE* 3.8 20.4 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.4 22.0 - - + -
149A LEU* 4.7 14.6 - - + -
187A SER* 4.8 4.5 - - - +
189A VAL* 6.0 1.8 - - + -
116B ILE* 3.2 3.5 - - - +
117B PHE* 2.6 65.4 + - + -
130B SER 4.4 9.0 - - - +
131B VAL* 1.3 79.4 - - - +
133B CYS* 1.3 71.2 + - - +
134B LEU* 5.1 2.2 - - + -
147B TRP* 3.8 3.6 - - - -
175B SER* 4.2 13.9 - - - +
176B SER 3.6 5.6 - - - +
177B THR* 4.0 16.2 - - + -
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Residues in contact with CYS 133 (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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114B VAL* 4.3 13.7 - - - -
115B PHE 3.3 9.6 - - - -
116B ILE* 4.7 0.9 - - - -
132B VAL* 1.3 76.1 - - - +
134B LEU* 1.3 62.3 + - - +
135B LEU* 4.1 10.1 + - + +
145B VAL* 4.5 0.9 - - + -
147B TRP* 3.5 18.1 - - + -
174B LEU 3.9 0.7 - - - +
175B SER* 3.7 4.5 - - - -
176B SER* 2.8 42.0 + - - +
193B CYS* 2.0 49.6 - - - -
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Residues in contact with LEU 134 (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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145A ALA* 4.2 13.7 - - + -
174A PHE* 3.7 23.6 - - + -
189A VAL* 4.1 25.1 - - + -
113B SER 3.4 2.3 - - - +
114B VAL* 3.1 6.3 - - - -
115B PHE* 2.6 67.3 + - + +
117B PHE* 3.7 13.7 - - + -
132B VAL* 5.1 2.5 - - + -
133B CYS* 1.3 74.5 - - - +
135B LEU* 1.3 75.7 + - - +
136B ASN* 3.8 22.8 + - + +
174B LEU 3.5 11.2 - - - +
175B SER* 5.0 0.9 - - - +
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Residues in contact with LEU 135 (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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112B PRO* 4.0 9.9 - - + -
113B SER 3.7 4.0 - - - -
114B VAL* 4.5 3.6 - - + +
133B CYS* 4.5 12.8 - - - +
134B LEU* 1.3 79.9 - - - +
136B ASN* 1.3 59.2 + - - +
138B PHE* 3.7 18.4 - - + -
143B ALA* 3.7 27.6 - - + -
145B VAL* 3.6 29.4 - - + -
173B SER* 3.6 2.4 - - - -
174B LEU* 3.0 43.9 + - + +
195B VAL* 3.6 39.0 - - + -
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Residues in contact with ASN 136 (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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172A HIS* 3.1 29.3 - - - -
189A VAL* 4.7 1.9 - - - +
191A THR* 3.4 31.5 + - - +
111B ALA 4.3 0.2 - - - +
112B PRO* 3.3 2.6 - - - +
113B SER* 2.9 45.2 + - - +
115B PHE* 4.6 1.8 - - + -
134B LEU* 4.1 24.0 - - + +
135B LEU* 1.3 72.9 - - - +
137B ASN* 1.3 93.1 + - - +
138B PHE* 3.7 1.8 - - - -
173B SER* 3.3 3.9 + - - -
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Residues in contact with ASN 137 (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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172A HIS* 3.0 25.2 + - - -
191A THR* 5.4 2.4 + - - +
110B ALA* 4.1 8.1 - - - +
111B ALA 3.7 11.4 - - - +
113B SER* 5.8 1.4 + - - -
136B ASN* 1.3 97.2 + - - +
138B PHE* 1.3 57.8 + - - +
166B ASP* 5.9 0.2 - - - -
169B ASP* 4.1 11.7 - - - +
171B THR* 3.4 26.1 + - + +
172B TYR 3.2 13.2 + - - -
173B SER* 3.2 3.0 + - - -
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Residues in contact with PHE 138 (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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110B ALA* 3.2 14.8 - - - +
112B PRO* 3.5 34.8 - - + -
135B LEU* 3.7 17.5 - - + -
137B ASN* 1.3 74.5 - - - +
139B TYR* 1.3 64.3 + - - +
140B PRO 3.4 13.9 - - - -
141B ARG* 3.4 27.6 - - - -
143B ALA* 3.9 12.1 - - + -
162B VAL* 5.3 0.7 - - + -
171B THR* 3.6 3.1 - - - -
172B TYR* 2.9 56.6 + - + +
173B SER 4.3 0.2 - - - -
174B LEU* 3.4 43.3 - - + -
197B HIS* 3.6 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