Contacts of the strand formed by residues 159 - 166 (chain B) in PDB entry 4YCV
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 GLU 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B ILE* 4.0 11.1 - - + +
113B PRO* 3.2 36.8 - - + +
116B ILE* 3.6 21.0 - - + +
155B VAL* 3.2 6.2 - - - +
156B GLY 2.9 32.2 + - - +
157B ASP 3.3 2.9 - - - +
158B GLY* 1.3 83.8 - - - +
160B LYS* 1.3 62.5 + - - +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 4.4 0.6 - - - +
116B ILE* 3.6 15.0 - - - +
153B ASP* 3.9 34.1 - - + +
154B LEU 3.4 5.2 - - - +
155B VAL* 4.1 14.4 - - + -
159B GLU* 1.3 79.6 - - - +
161B ILE* 1.3 76.1 + - - +
162B GLN* 5.7 1.1 - - - +
203B GLU* 4.5 20.2 + - - -
204B LEU* 6.0 0.3 - - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 3.9 11.2 - - + +
115B PHE* 3.7 28.3 - - + -
116B ILE* 3.6 20.9 - - + -
135B ILE* 3.6 30.5 - - + -
153B ASP* 3.7 2.4 - - - -
154B LEU* 2.8 54.5 + - + +
160B LYS* 1.3 85.1 - - - +
162B GLN* 1.3 60.9 + - - +
204B LEU* 4.3 11.7 - - + +
206B ILE* 3.7 25.6 - - + -
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Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 3.0 40.2 - - - +
152B PHE 3.1 11.8 - - - +
153B ASP* 4.0 8.7 + - - +
160B LYS* 4.7 2.5 - - - +
161B ILE* 1.3 73.4 - - - +
163B VAL* 1.3 62.1 + - - +
164B LEU* 5.0 1.1 - - - -
199B SER* 3.9 12.4 + - - -
203B GLU* 3.6 35.1 + - + +
204B LEU 3.4 8.3 + - - +
205B SER* 3.1 33.6 + - - +
206B ILE* 2.9 28.4 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 5.0 1.1 - - + -
150B ARG 3.5 1.9 - - - +
151B PHE* 3.3 7.1 - - - -
152B PHE* 2.9 61.8 + - + -
154B LEU* 3.5 31.6 - - + -
162B GLN* 1.3 71.8 - - - +
164B LEU* 1.3 61.0 + - - +
165B ALA* 3.7 0.6 + - + +
181B TYR* 5.5 0.4 - - + -
192B ILE* 3.7 24.5 - - + -
206B ILE* 3.5 13.0 - - + +
208B PRO* 3.8 28.5 - - + -
211B THR* 5.2 1.6 - - + +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.6 25.8 - - + -
150B ARG 3.5 2.7 - - - -
151B PHE* 3.5 32.5 - - + -
162B GLN* 3.8 2.2 + - - +
163B VAL* 1.3 71.8 - - - +
165B ALA* 1.3 57.7 + - - +
166B ASN* 3.6 14.3 + - + +
199B SER* 4.8 12.8 - - - +
205B SER* 4.3 16.4 - - - +
206B ILE 3.0 7.1 + - - -
207B PHE* 3.2 49.4 - - + -
208B PRO* 3.1 16.4 - - - +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.5 6.8 - - - +
150B ARG* 2.9 45.1 + - + +
152B PHE* 4.7 4.3 - - + -
163B VAL* 3.7 1.6 + - + -
164B LEU* 1.3 71.5 - - - +
166B ASN* 1.3 62.2 + - - +
170B HIS* 6.4 0.2 - - + -
177B PHE* 3.8 8.2 - - + -
181B TYR* 3.5 39.7 - - + -
208B PRO* 3.9 12.3 - - + +
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Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS* 4.1 3.3 - - - +
149B LEU* 4.1 13.9 - - - +
164B LEU* 3.6 13.9 + - + +
165B ALA* 1.3 72.3 - - - +
167B TYR* 1.3 76.5 + - - +
168B SER* 3.1 22.6 + - - -
169B PHE* 3.2 44.4 + - + +
170B HIS* 3.1 23.2 + - - +
177B PHE* 4.1 1.8 - - - -
207B PHE* 6.0 0.2 - - - -
208B PRO 4.8 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