Contacts of the strand formed by residues 185 - 190 (chain A) in PDB entry 4NYK
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 PHE 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.7 32.3 - + - -
166A ILE* 4.2 12.3 - - + +
170A LEU* 3.7 29.8 - - + -
173A CYS* 4.0 13.9 - - - -
180A CYS* 4.4 0.2 - - + -
181A SER 3.3 20.6 - - - -
182A PRO* 2.9 21.9 + - + +
183A GLU 3.2 3.7 - - - +
184A ASP* 1.3 80.3 - - - +
186A LYS* 1.3 61.1 + - - +
187A VAL* 3.9 3.5 + - - +
196A TYR* 4.1 19.3 - - + -
197A THR 3.4 2.9 - - - -
198A PHE* 3.5 46.4 - + + -
219A LEU* 5.3 0.2 - - + -
221A ILE* 4.2 12.1 - - + -
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Residues in contact with LYS 186 (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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184A ASP 4.2 0.8 + - - -
185A PHE* 1.3 72.6 - - - +
187A VAL* 1.3 76.8 + - - +
188A VAL* 3.4 4.0 + - + +
196A TYR* 3.2 3.8 - - - -
197A THR* 2.7 46.1 + - - +
200A ALA* 3.9 17.9 - - + -
202A GLN* 3.1 31.0 + - - +
203A ASP* 3.7 32.4 + - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 5.2 0.9 - - - +
185A PHE 3.9 3.3 + - - +
186A LYS* 1.3 88.9 - - - +
188A VAL* 1.3 62.9 + - - +
189A PHE* 3.7 29.2 - - + -
194A LYS* 3.9 24.0 - - + -
195A CYS 3.4 9.2 - - - +
196A TYR* 3.7 23.1 - - + -
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Residues in contact with VAL 188 (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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92A THR* 3.9 16.4 - - + -
186A LYS* 4.5 2.9 - - + +
187A VAL* 1.3 74.8 - - - +
189A PHE* 1.3 77.2 + - - +
190A THR* 4.7 1.6 - - + -
195A CYS* 2.7 51.3 + - + +
196A TYR 4.0 0.4 - - - +
197A THR* 3.3 26.9 - - - +
257A PRO* 4.3 21.5 - - + -
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Residues in contact with PHE 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 LEU* 3.7 19.1 - - + -
159A TYR* 3.5 26.7 - - + -
160A ASP* 3.7 35.0 - - + -
187A VAL* 3.7 20.9 - - + -
188A VAL* 1.3 85.0 - - - +
190A THR* 1.3 63.8 - - - +
193A GLY 3.2 15.9 - - - -
194A LYS* 4.1 10.3 - - + -
257A PRO* 5.8 0.2 - - - +
327A VAL* 3.6 30.7 - - + +
328A HIS* 3.2 21.8 - - + +
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Residues in contact with THR 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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92A THR* 4.9 1.3 - - + -
94A CYS* 3.5 2.1 - - - -
159A TYR* 5.5 1.9 - - - -
188A VAL* 4.6 4.5 - - + +
189A PHE* 1.3 79.9 - - - +
191A ARG* 1.3 59.1 + - - +
192A TYR* 2.9 15.7 + - - +
193A GLY* 3.0 19.9 + - - -
195A CYS* 3.2 29.9 - - + -
257A PRO* 4.3 25.4 - - + +
259A ILE* 3.9 23.8 - - + +
260A ASP* 6.3 0.2 - - - -
327A VAL* 5.4 2.6 - - - +
328A HIS* 3.5 19.3 + - - +
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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