Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 1O9H
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 VAL 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 4.0 29.2 - - + +
46A ARG* 3.8 26.7 - - + -
47A LEU* 3.9 18.6 - - + -
170A ASP 3.0 8.4 + - - +
171A VAL* 3.4 4.4 - - + +
172A VAL* 2.8 26.7 + - - +
208A ALA* 1.3 77.1 - - - +
210A ILE* 1.3 66.8 + - - +
211A ALA 4.9 0.2 - - - +
227A LEU* 4.9 4.0 - - + -
239A LEU* 4.2 23.1 - - + -
240A VAL 3.5 7.9 - - - +
241A ARG* 3.9 14.4 - - - +
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Residues in contact with ILE 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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172A VAL* 3.4 22.4 - - + -
197A LEU* 4.1 25.4 - - + +
200A LEU* 4.1 17.0 - - + -
201A ALA* 4.7 7.0 - - + -
204A LEU* 3.8 30.5 - - + -
208A ALA 4.8 1.3 - - - +
209A VAL* 1.3 77.7 - - - +
211A ALA* 1.3 61.5 + - - +
212A VAL* 4.1 12.5 - - + +
238A VAL 3.5 2.1 - - - +
239A LEU* 3.2 5.8 - - - -
240A VAL* 2.8 56.1 + - + +
242A ALA* 4.6 12.8 - - - +
245A VAL* 4.7 2.2 - - + -
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Residues in contact with ALA 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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39A ILE* 3.5 22.7 - - + +
43A ALA* 5.0 7.6 - - + -
171A VAL* 5.5 0.2 - - + -
172A VAL 2.7 14.3 + - - +
173A LEU* 3.3 11.0 - - + +
174A THR* 3.0 25.5 + - - +
209A VAL* 4.2 0.4 - - + -
210A ILE* 1.3 74.3 - - - +
212A VAL* 1.3 62.3 + - - +
213A THR* 5.0 0.9 - - - -
239A LEU* 3.2 28.7 - - + -
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Residues in contact with VAL 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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39A ILE* 6.2 0.2 - - - -
174A THR* 3.4 20.9 - - + +
176A LEU* 4.6 12.1 - - + -
193A VAL* 5.5 6.1 - - + -
196A LEU* 4.7 17.0 - - + -
197A LEU* 4.8 8.1 - - + -
200A LEU* 5.8 0.9 - - + -
210A ILE* 4.2 18.8 - - + +
211A ALA* 1.3 75.0 - - - +
213A THR* 1.3 62.2 + - - +
219A ILE* 3.7 14.3 - - + +
237A ALA* 3.2 24.8 - - - +
238A VAL* 3.2 34.1 + - + +
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Residues in contact with THR 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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31A PHE* 4.2 8.2 - - + -
35A LEU* 4.9 1.3 - - + -
39A ILE* 3.8 31.3 - - + +
173A LEU* 4.7 6.1 - - - +
174A THR 3.2 15.0 + - - -
175A ASP* 3.4 15.8 - - - +
176A LEU* 3.1 29.4 + - - +
211A ALA 4.8 0.5 + - - -
212A VAL* 1.3 75.9 - - - +
214A ASP* 1.3 61.2 + - - +
219A ILE* 4.2 1.6 - - - -
230A LEU* 5.9 0.2 - - + -
235A ARG* 3.5 24.7 - - + -
236A SER 3.3 15.0 - - - +
237A ALA* 4.1 6.1 - - + -
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Residues in contact with ASP 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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175A ASP* 4.6 2.9 - - - -
176A LEU* 3.7 25.8 - - + +
181A ARG* 3.5 25.0 + - - +
187A GLN* 3.4 15.9 - - - +
188A VAL* 3.2 29.7 + - - +
213A THR* 1.3 72.5 - - - +
215A ARG* 1.3 65.1 + - - +
216A SER* 3.2 11.4 + - - +
219A ILE* 3.9 15.4 - - + +
235A ARG* 3.4 11.9 - - - -
236A SER 3.0 30.7 + - - -
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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