Contacts of the strand formed by residues 172 - 179 (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 TYR 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A HIS* 5.8 0.2 - - - -
102B LYS* 5.4 3.5 + - - -
104B GLU* 4.8 11.8 + - - +
137B ASN* 3.2 3.7 + - - -
138B PHE* 2.9 56.3 + - + +
139B TYR* 3.6 29.2 - + - -
141B ARG* 3.9 39.5 - - + +
162B VAL* 4.3 5.6 - - + -
163B THR* 3.6 22.2 - - - +
164B GLU* 4.4 7.0 - - - -
165B GLN* 3.4 46.0 + - + +
171B THR* 1.3 76.1 - - - +
173B SER* 1.3 67.3 + - - +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A HIS* 3.0 37.2 + - - -
174A PHE* 3.2 12.4 - - - -
135B LEU 3.6 8.5 - - - -
136B ASN* 3.3 2.6 + - - -
137B ASN* 3.2 11.1 + - - -
138B PHE* 3.7 2.0 - - - -
162B VAL* 3.5 1.5 - - - +
163B THR* 2.6 52.8 + - - +
172B TYR* 1.3 79.8 + - - +
174B LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.7 2.9 - - - -
133B CYS 3.9 0.2 - - - +
134B LEU* 3.5 5.2 - - - +
135B LEU* 3.0 41.5 + - + +
138B PHE* 3.4 19.4 - - + -
141B ARG* 2.9 33.4 - - - +
143B ALA* 4.6 8.3 - - + +
145B VAL* 4.0 23.6 - - + -
160B GLU* 3.6 35.9 - - + +
161B SER 3.4 7.9 - - - +
162B VAL* 3.9 8.5 - - + -
173B SER* 1.3 75.1 - - - +
175B SER* 1.3 69.9 + - - +
176B SER* 4.1 2.2 - - - +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.6 36.4 - - - -
187A SER* 4.3 8.0 - - - -
132B VAL* 4.2 11.2 - - - +
133B CYS 3.7 4.0 - - - -
134B LEU* 5.0 1.8 - - - +
159B GLN 3.7 1.0 - - - +
160B GLU* 3.4 4.0 - - - -
161B SER* 2.8 40.9 + - - -
174B LEU* 1.3 77.4 - - - +
176B SER* 1.3 61.1 + - - +
177B THR* 3.7 17.9 + - - +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.6 0.5 - - - -
133B CYS* 2.8 41.5 + - - -
145B VAL* 4.1 22.0 - - - +
147B TRP* 2.9 28.6 + - - -
158B SER* 4.5 4.0 - - - -
159B GLN 3.4 9.1 + - - -
160B GLU* 4.7 6.0 + - - +
174B LEU* 4.1 10.1 - - - +
175B SER* 1.3 75.3 + - - +
177B THR* 1.3 61.8 + - - +
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Residues in contact with THR 177 (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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149A LEU* 5.4 7.4 - - + +
187A SER* 5.3 5.4 - - - +
130B SER* 5.0 6.3 + - - -
131B VAL 3.3 8.7 - - - -
132B VAL* 4.0 16.6 - - + -
147B TRP* 4.5 0.4 - - - -
158B SER* 3.2 4.8 - - - -
159B GLN* 3.0 39.6 + - + +
161B SER* 6.4 0.9 - - - -
175B SER* 3.7 17.7 - - - +
176B SER* 1.3 77.0 - - - +
178B LEU* 1.3 59.3 + - - +
179B THR* 3.9 11.1 + - - -
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Residues in contact with LEU 178 (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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129B ALA 3.9 0.7 - - - +
130B SER* 3.6 3.6 - - - -
131B VAL* 2.7 44.4 + - + +
147B TRP* 3.6 46.5 - - + -
149B VAL* 4.2 23.1 - - + -
154B GLN* 3.8 8.1 - - + -
157B ASN* 3.4 40.6 - - - +
158B SER* 3.9 5.8 - - - +
177B THR* 1.3 71.7 - - - +
179B THR* 1.3 60.2 + - - +
180B LEU* 4.0 21.2 + - + -
191B TYR* 4.9 2.0 - - + -
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Residues in contact with THR 179 (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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151A LYS* 5.0 4.4 - - - +
179A GLN* 4.7 10.6 + - - +
128B THR* 4.5 12.6 - - - +
129B ALA 3.9 5.2 - - - +
130B SER* 3.5 16.8 + - - +
157B ASN* 3.0 31.4 + - - +
158B SER* 4.7 0.2 - - - +
159B GLN* 5.3 7.4 + - - -
177B THR* 3.9 9.8 + - - -
178B LEU* 1.3 74.4 - - - +
180B LEU* 1.3 74.7 + - - +
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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