Contacts of the strand formed by residues 208 - 217 (chain A) in PDB entry 1OWI
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 ARG 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TRP* 6.0 2.6 - - - -
118A THR* 3.6 9.5 + - - -
119A ILE* 3.6 13.1 - - - +
120A CYS* 3.1 41.7 - - + +
204A SER* 4.3 1.1 - - - -
205A LEU 3.1 24.1 + - - +
206A GLN 3.6 1.4 + - - -
207A GLY* 1.3 76.7 - - - +
209A MET* 1.3 101.2 + - - +
210A THR* 3.0 20.3 + - - +
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Residues in contact with MET 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.5 28.0 - - + -
119A ILE* 5.0 5.8 - - + +
120A CYS* 4.3 3.6 + - - +
135A GLU* 3.7 12.3 - - - +
202A VAL* 3.4 27.4 - - + -
203A CYS 4.0 5.2 - - - -
204A SER* 4.2 17.4 + - - +
207A GLY 4.0 3.0 + - - +
208A ARG* 1.3 113.6 + - - +
210A THR* 1.3 57.1 + - - +
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 5.5 0.7 - - - -
120A CYS* 3.5 14.1 + - - +
121A LEU 3.9 1.6 + - - -
122A PRO* 3.5 38.1 - - + -
202A VAL* 3.1 8.7 - - - +
203A CYS 2.8 45.4 + - - +
205A LEU* 4.4 15.2 + - + +
208A ARG* 3.0 19.6 + - - +
209A MET* 1.3 72.7 + - - +
211A LEU* 1.3 65.2 + - - +
212A THR* 3.1 12.3 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 3.8 15.3 - - - +
35A MET* 4.1 7.4 - - - -
41A ILE* 3.8 30.1 - - + -
119A ILE* 3.8 22.1 - - + +
120A CYS 3.0 18.7 + - - +
121A LEU* 4.5 6.7 - - + -
122A PRO* 3.0 21.7 - - - +
200A PRO* 3.7 17.3 - - + -
201A LEU 3.7 27.8 - - - +
202A VAL* 4.6 4.9 - - + +
210A THR* 1.3 69.0 - - - +
212A THR* 1.3 59.0 + - - +
213A GLY 3.9 7.9 - - - +
214A ILE* 5.4 4.5 - - + -
233A VAL* 3.6 12.5 - - + +
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO* 4.8 3.7 - - - +
127A ASP* 4.5 12.1 - - - +
128A PRO* 4.1 25.3 - - + +
181A LEU* 3.4 27.2 - - + +
201A LEU* 2.9 8.2 + - + -
203A CYS* 3.4 34.7 - - - +
210A THR* 3.1 14.5 + - - +
211A LEU* 1.3 74.0 - - - +
213A GLY* 1.3 59.0 + - - +
231A THR 3.4 8.3 - - - +
232A ARG* 4.1 4.7 - - + +
233A VAL* 3.4 14.1 + - - +
234A SER 5.0 0.7 + - - -
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 5.5 1.1 - - - -
199A GLY 3.6 0.5 - - - +
201A LEU* 2.9 41.8 + - - +
211A LEU* 3.6 7.1 - - - +
212A THR* 1.3 81.1 - - - +
214A ILE* 1.3 65.7 + - - -
230A TYR* 4.1 9.2 - - - -
231A THR 3.1 12.3 - - - -
233A VAL* 3.8 2.9 - - - +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 6.2 0.2 - - - +
41A ILE* 4.0 22.9 - - + +
42A SER* 3.2 31.4 - - - +
43A ALA* 4.2 4.0 - - + +
96A ASP 4.5 0.9 - - - +
97A ILE* 3.8 26.0 - - + -
198A GLY* 3.3 36.3 - - - +
199A GLY 3.5 3.8 - - - -
211A LEU* 5.4 4.7 - - + -
213A GLY* 1.3 78.0 - - - -
215A VAL* 1.3 68.3 + - - +
216A SER* 3.2 1.4 + - - -
230A TYR* 3.1 7.7 - - - -
231A THR* 3.0 36.4 + - - +
233A VAL* 4.4 12.1 - - + -
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 4.1 5.5 - - - +
45A HIS* 4.4 0.3 - - - -
96A ASP 5.7 0.2 - - - +
136A ILE* 4.9 8.3 - - + -
137A THR 5.8 0.9 - - - +
192A SER* 4.2 13.7 - - - +
196A ASP* 3.5 9.0 - - + +
197A SER* 3.7 19.3 - - - +
198A GLY* 2.7 33.6 + - - +
199A GLY* 3.1 29.1 + - - +
200A PRO 5.4 0.4 - - - +
214A ILE* 1.3 73.8 - - - +
216A SER* 1.3 60.7 + - - +
229A VAL 5.0 0.2 - - - +
230A TYR* 3.3 28.3 - - + +
245A 426 3.9 24.2 - - + -
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A HIS* 3.4 21.4 + - - -
93A HIS* 3.6 10.7 + - - +
96A ASP* 2.9 25.9 + - - +
180A MET* 6.5 0.2 - - - -
197A SER* 4.8 0.2 + - - -
214A ILE 3.2 7.8 + - - -
215A VAL* 1.3 75.1 - - - +
217A TRP* 1.3 84.0 + - - +
229A VAL 3.2 11.7 + - - -
230A TYR* 4.2 7.6 - - - -
231A THR* 4.3 11.4 - - - -
245A 426 4.0 11.3 - - - -
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Residues in contact with TRP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.4 40.4 - - + +
92A ALA* 3.5 20.6 - - + -
93A HIS* 3.5 28.3 - - + +
172A TYR* 3.3 46.7 - + + -
175A GLU* 4.8 2.9 - - + -
176A VAL* 4.5 9.6 - - + -
180A MET* 3.9 16.5 - - - +
216A SER* 1.3 106.8 - - - +
218A GLY* 1.3 73.6 + - - +
228A GLY* 3.9 0.9 - - - -
229A VAL* 2.8 65.8 + - + +
245A 426 3.9 16.1 - - + -
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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
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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