Contacts of the strand formed by residues 188 - 196 (chain A) in PDB entry 4Y2H
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 SER 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A TRP* 5.9 0.2 - - - -
186A PRO* 3.6 2.3 - - - +
187A ALA* 1.3 81.7 - - - +
189A ALA* 1.3 61.6 + - - +
190A GLU* 5.2 2.4 + - - -
255A GLN* 4.0 12.5 + - - -
256A LEU 3.1 15.3 - - - -
257A GLU* 3.9 19.3 - - - -
258A LEU* 4.2 5.8 - - - +
294A VAL* 3.2 8.4 - - - +
295A THR* 3.0 43.3 + - - -
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Residues in contact with ALA 189 (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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156A TRP* 4.2 13.2 - - + -
161A LEU* 4.0 24.9 - - + -
188A SER* 1.3 75.1 - - - +
190A GLU* 1.3 66.1 + - - +
255A GLN* 4.4 1.0 - - - -
256A LEU* 2.6 47.4 + - + +
258A LEU* 4.4 0.6 - - + +
293A GLN 3.2 10.8 - - - +
294A VAL* 3.9 12.8 - - + -
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Residues in contact with GLU 190 (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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161A LEU* 5.1 1.1 - - - -
188A SER* 5.2 2.5 + - - +
189A ALA* 1.3 80.7 - - - +
191A LEU* 1.3 64.0 + - - +
192A PHE* 3.8 20.6 - - + -
252A ARG* 2.5 38.5 + - - -
254A ALA 3.4 6.1 - - - +
255A GLN* 3.8 24.6 + - + +
292A PHE* 3.1 27.6 - - - +
293A GLN* 2.8 42.6 + - + +
295A THR* 4.3 8.3 + - - -
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Residues in contact with LEU 191 (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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160A GLY 4.0 10.8 - - - +
161A LEU* 3.7 42.2 - - + -
162A LEU* 4.7 1.1 - - + -
190A GLU* 1.3 71.7 - - - +
192A PHE* 1.3 62.3 + - - +
252A ARG* 3.2 9.5 - - - +
253A PHE* 2.9 53.3 + - + -
254A ALA* 2.9 17.6 + - + -
256A LEU* 5.7 0.7 - - + -
271A VAL* 3.8 22.0 - - + -
290A ILE* 4.5 5.2 - - + -
291A TRP 3.4 17.5 - - - +
292A PHE* 4.0 2.7 - - + -
343A LEU* 3.6 23.3 - - + -
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Residues in contact with PHE 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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190A GLU* 3.8 30.7 - - + -
191A LEU* 1.3 74.0 - - - +
193A ILE* 1.3 62.1 + - - +
250A PRO* 4.7 9.0 - - + -
251A GLN 3.2 7.9 - - - +
252A ARG* 3.6 35.0 - - + -
253A PHE* 3.6 2.9 - - - -
290A ILE* 3.0 29.1 - - - +
291A TRP* 2.9 53.7 + + + +
292A PHE* 4.3 0.4 - - - -
293A GLN* 3.7 41.1 - - + -
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Residues in contact with ILE 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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192A PHE* 1.3 75.5 - - - +
194A ALA* 1.3 65.4 + - - +
250A PRO* 4.5 1.3 - - - -
251A GLN* 2.8 47.2 + - + +
253A PHE* 3.7 16.2 - - + -
275A PHE* 3.8 48.2 - - + -
288A PHE* 3.8 33.9 - - + -
289A ALA 3.4 10.3 - - - +
290A ILE* 3.9 3.1 - - + -
291A TRP* 5.0 1.3 - - - -
341A ILE* 4.0 23.1 - - + -
357A LEU* 4.6 3.4 - - + -
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Residues in contact with ALA 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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193A ILE* 1.3 77.7 - - - +
195A PRO* 1.3 79.5 - - + +
196A ILE* 3.7 1.9 - - + +
246A VAL* 4.1 17.5 - - + -
248A ALA 4.2 1.3 - - - +
249A ARG 5.1 0.2 - - - -
250A PRO* 4.1 9.6 - - + -
288A PHE* 3.3 7.8 - - - -
289A ALA 3.0 30.3 + - - -
291A TRP* 3.9 24.7 - - + -
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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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194A ALA* 1.3 87.5 - - + +
196A ILE* 1.3 61.8 + - - +
246A VAL* 4.0 0.7 - - - -
247A LEU* 3.0 31.5 + - + -
248A ALA* 3.5 28.0 - - + +
249A ARG 5.2 0.4 - - - +
275A PHE* 6.2 0.4 - - + -
277A CYS* 3.6 25.6 - - - -
279A CYS* 4.5 6.3 - - - -
285A MET* 3.7 28.9 - - + -
287A GLY 3.4 8.1 - - - +
288A PHE* 3.8 11.6 - - + -
337A VAL* 4.5 3.8 - - + -
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Residues in contact with ILE 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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194A ALA* 3.7 9.9 - - + +
195A PRO* 1.3 81.8 - - - +
197A SER* 1.3 60.6 + - - +
198A ASP* 4.1 23.6 - - + +
241A LEU* 3.7 28.9 - - + -
245A ASP 3.2 12.8 - - - +
246A VAL* 4.3 13.0 - - + -
247A LEU* 3.5 6.5 - - - -
285A MET* 3.5 5.2 - - - +
286A HIS* 2.9 29.4 + - + -
287A GLY 2.8 31.0 + - - +
288A PHE 3.7 16.8 - - - +
289A ALA* 3.8 7.4 - - + +
322A LEU* 4.7 3.8 - - + -
324A TYR* 4.5 9.6 - - + -
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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