Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 1OKM
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.6 16.4 - - + +
45A LYS 2.9 24.7 + - - -
46A PRO* 4.9 2.2 - - + -
47A LEU* 3.8 23.6 - - + -
82A GLY* 3.2 10.2 - - - -
83A PRO* 3.6 21.8 - - + +
189A LEU 3.2 16.8 - - - +
190A ASP* 1.3 75.1 - - - +
192A TRP* 1.3 72.6 + - - +
193A THR* 4.0 14.4 - - + -
210A ILE* 3.7 25.1 - - + -
211A VAL 3.2 13.7 - - - +
212A LEU* 4.0 5.2 - - + -
213A LYS 4.2 2.0 - - - +
258A ALA* 3.6 2.4 - - - -
259A SER* 3.0 51.5 + - - -
260A PHE* 3.7 6.2 - - - -
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Residues in contact with TRP 192 (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 ILE* 3.7 39.8 - - + +
35A THR* 3.7 25.0 + - + +
38A ALA* 4.2 13.9 - - + +
109A VAL* 3.9 34.5 - - + -
147A PHE* 4.4 2.9 - + - -
191A TYR* 1.3 75.9 - - - +
193A THR* 1.3 60.7 + - - +
194A TYR* 5.5 1.5 - - + -
209A TRP 3.7 0.2 - - - +
210A ILE* 3.5 3.8 - - - -
211A VAL* 2.8 48.7 + - + +
212A LEU 4.0 4.7 - - - -
213A LYS* 3.6 33.9 - - + -
256A ILE* 3.8 12.6 - - + -
257A LYS 3.2 6.5 - - - -
258A ALA* 3.7 23.1 - - + +
260A PHE* 3.4 27.2 - + - -
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Residues in contact with THR 193 (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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44A LEU* 4.3 7.0 - - + -
83A PRO* 3.5 30.1 - - + +
191A TYR* 4.0 22.7 - - + -
192A TRP* 1.3 75.3 - - - +
194A TYR* 1.3 65.9 + - - +
208A THR* 3.9 8.8 - - - +
209A TRP 2.9 17.6 + - - -
210A ILE* 4.2 1.2 - - - +
255A GLN 4.0 1.0 - - - +
256A ILE* 3.6 1.1 - - - -
257A LYS* 2.8 53.6 + - + +
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Residues in contact with TYR 194 (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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29A SER* 2.8 26.7 + - - -
31A VAL* 3.5 26.5 + - + +
33A ILE* 5.7 3.1 - - + -
107A HIS* 2.6 33.6 + + - -
192A TRP* 5.5 1.1 - - + -
193A THR* 1.3 83.8 + - - +
195A PRO* 1.3 89.5 - - + +
196A GLY* 3.6 2.2 + - - -
208A THR* 3.9 2.9 - - - -
209A TRP* 3.0 48.9 + + + +
211A VAL* 4.8 4.9 - - + -
251A LEU* 4.9 3.4 - - + -
254A ARG* 3.4 28.0 - - + -
255A GLN 4.0 11.0 - - - +
256A ILE* 4.0 19.5 - - + -
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Residues in contact with PRO 195 (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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27A ARG* 3.9 24.7 - - + +
194A TYR* 1.3 88.5 - - + +
196A GLY* 1.3 58.8 + - - +
207A VAL 3.7 5.6 - - - +
208A THR* 4.7 5.2 - - + +
254A ARG* 2.9 43.4 + - + -
255A GLN 4.6 7.9 - - - +
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Residues in contact with GLY 196 (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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27A ARG* 3.0 40.5 + - - -
29A SER* 3.3 13.7 - - - -
194A TYR* 3.6 3.0 + - - -
195A PRO* 1.3 74.6 - - - +
197A SER* 1.3 58.6 + - - -
205A GLU* 3.6 2.1 - - - -
207A VAL* 2.7 22.1 + - - +
209A TRP* 3.8 4.9 - - - -
254A ARG* 3.8 2.5 - - - -
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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