Contacts of the strand formed by residues 191 - 200 (chain A) in PDB entry 2P7I
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 GLN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLY 3.9 0.8 + - - -
190A LEU* 1.3 71.1 - - - +
192A VAL* 1.3 83.3 + - - +
193A THR* 3.3 14.4 + - - +
243A CYS* 3.2 3.9 - - - -
244A GLU* 2.8 46.4 + - + +
245A LYS 4.1 11.2 - - - +
246A GLY* 4.1 4.5 - - - +
34B ARG* 4.4 15.6 - - - +
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Residues in contact with VAL 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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182A GLU* 3.8 26.7 - - + +
185A ALA* 3.9 24.9 - - + -
186A SER* 4.8 4.7 - - - +
190A LEU 3.8 3.9 + - - +
191A GLN* 1.3 87.6 + - - +
193A THR* 1.3 60.5 + - - +
194A TYR 4.0 15.0 - - - +
195A ARG* 3.3 46.8 + - + +
241A LEU* 4.1 15.0 - - + -
242A LEU 4.0 2.2 - - - +
243A CYS* 4.1 7.0 - - - -
34B ARG* 5.2 2.4 + - - -
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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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191A GLN* 3.3 15.3 + - - +
192A VAL* 1.3 75.3 - - - +
194A TYR* 1.3 66.4 + - + +
195A ARG* 3.7 6.1 + - - -
242A LEU* 2.8 24.1 + - + -
244A GLU* 2.9 35.3 + - - +
34B ARG* 5.8 1.3 + - - +
38B PRO* 3.8 29.2 - - + -
226B TYR* 4.5 5.5 + - - -
230B GLN* 3.7 10.6 + - - -
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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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39A PHE* 4.0 13.9 - + + -
192A VAL* 4.0 2.3 - - - +
193A THR* 1.3 84.4 - - + +
195A ARG* 1.3 68.8 + - - +
196A SER* 4.3 0.4 - - - -
240A PHE* 3.9 0.6 - - + +
241A LEU* 3.4 4.5 - - - -
242A LEU* 2.9 45.1 + - + +
35B ALA* 2.9 41.1 + - - +
38B PRO* 3.7 24.7 - - + -
39B PHE* 3.7 7.9 - + - -
194B TYR* 3.2 38.6 - + - +
196B SER* 3.8 13.1 + - - -
226B TYR* 4.4 1.1 - - - -
230B GLN* 3.4 26.0 + - - -
240B PHE* 3.5 18.0 - - - -
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Residues in contact with ARG 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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178A LEU* 4.2 2.9 - - + -
182A GLU* 2.8 37.3 + - - +
191A GLN* 5.6 0.2 - - - +
192A VAL* 3.3 24.7 + - + +
193A THR 3.7 13.7 + - - -
194A TYR* 1.3 77.1 - - - +
196A SER* 1.3 64.4 + - - +
233A PRO* 5.2 0.9 - - - -
240A PHE 3.6 4.5 - - - -
241A LEU* 3.7 21.1 - - + -
34B ARG* 5.5 1.4 - - - +
194B TYR* 3.9 5.8 + - - -
196B SER* 5.3 0.5 + - - -
226B TYR* 4.9 3.6 - - - -
227B GLN* 3.3 54.1 + - - +
230B GLN* 2.8 58.0 + - + +
231B GLN* 3.7 28.2 - - + +
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Residues in contact with SER 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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178A LEU* 4.2 4.4 - - - +
194A TYR* 6.0 0.4 - - - -
195A ARG* 1.3 77.8 - - - +
197A GLY* 1.3 72.1 + - - +
230A GLN* 4.5 13.3 + - - +
233A PRO* 3.7 18.1 - - - +
239A ILE* 3.6 6.4 - - - +
240A PHE* 2.8 48.0 + - - +
194B TYR* 3.3 29.8 + - - -
195B ARG 5.4 0.2 + - - -
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Residues in contact with GLY 197 (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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196A SER* 1.3 86.1 + - - +
198A ILE* 1.3 66.8 + - - +
199A PHE 4.2 0.3 + - - -
226A TYR* 5.4 1.7 - - - +
229A GLY 4.3 4.4 + - - +
230A GLN* 4.3 13.0 + - - +
233A PRO* 3.6 13.9 - - - +
236A CYS* 3.5 21.8 - - - -
238A SER 3.4 10.1 - - - -
239A ILE* 4.4 0.7 - - - -
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Residues in contact with ILE 198 (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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28A MSE 3.6 15.9 - - + +
31A PHE* 3.8 35.9 - - + +
32A MSE 3.8 24.7 - - + +
35A ALA* 3.9 25.1 - - + -
36A PHE* 4.5 1.3 - - + -
139A VAL* 4.2 15.3 - - + -
197A GLY* 1.3 76.9 - - - +
199A PHE* 1.3 72.2 + - + +
226A TYR* 4.5 7.0 - - + -
236A CYS* 3.5 1.4 - - - +
237A ALA* 3.4 1.7 + - - +
238A SER* 2.9 30.8 + - - +
240A PHE* 4.0 26.5 - - + -
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Residues in contact with PHE 199 (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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23A PHE* 3.5 27.8 - + - -
27A VAL* 3.9 7.2 - - + -
28A MSE 3.6 17.9 - - - -
31A PHE* 3.7 30.7 - + + -
197A GLY 4.0 0.4 + - - -
198A ILE* 1.3 76.5 - - + +
200A PHE* 1.3 77.6 + - - +
201A LYS* 3.1 7.9 + - + -
208A TRP* 3.6 19.7 - + - -
222A LEU* 3.6 31.6 - - + -
225A CYS* 3.5 30.7 + - + -
226A TYR* 4.2 12.2 + - - +
229A GLY* 4.7 1.6 - - - -
236A CYS* 3.3 7.1 - - - -
237A ALA* 2.7 30.8 + - - +
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Residues in contact with PHE 200 (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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146A VAL* 3.9 20.2 - - + -
199A PHE* 1.3 82.8 - - - +
201A LYS* 1.3 61.3 + - - +
202A ALA* 4.0 11.8 + - + -
208A TRP* 4.8 0.9 - - - -
225A CYS* 2.9 40.5 + - - +
228A LEU* 4.1 24.0 - - + -
229A GLY* 3.8 15.5 - - - +
232A TYR* 4.0 27.8 - + + -
235A LEU* 3.9 36.3 - - + -
236A CYS* 4.5 4.3 - - - +
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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