Contacts of the strand formed by residues 159 - 166 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 4.0 5.2 - - + +
113A PRO* 3.7 30.3 - - + +
116A ILE* 3.8 26.9 - - + +
155A VAL* 3.4 4.6 - - - +
156A GLY 2.9 32.0 + - - +
157A ASP 4.1 5.7 - - - +
158A GLY* 1.3 85.5 - - - +
160A LYS* 1.3 63.3 + - - +
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Residues in contact with LYS 160 (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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112A ILE* 4.3 2.2 - - - +
116A ILE* 3.9 8.8 - - - +
140A MET* 5.4 3.8 - - - +
141A ARG* 6.1 0.2 - - - +
153A ASP* 3.6 32.6 + - + +
154A LEU 3.5 9.2 - - - +
155A VAL* 3.6 24.0 - - + +
159A GLU* 1.3 79.7 - - - +
161A ILE* 1.3 77.3 + - - +
203A GLU* 5.7 1.7 - - - +
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Residues in contact with ILE 161 (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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112A ILE* 3.6 19.9 - - + +
115A PHE* 3.9 23.3 - - + -
116A ILE* 3.7 20.2 - - + -
135A ILE* 3.9 26.5 - - + -
153A ASP 3.8 0.2 - - - -
154A LEU* 2.9 50.4 + - + +
160A LYS* 1.3 85.8 - - - +
162A GLN* 1.3 61.4 + - - +
203A GLU* 5.8 1.3 - - - -
204A LEU* 4.4 11.9 - - + +
205A SER* 5.1 0.2 - - - -
206A ILE* 3.8 28.0 - - + -
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Residues in contact with GLN 162 (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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151A PHE* 3.1 38.2 - - + +
152A PHE 3.5 13.0 - - - +
153A ASP* 4.0 11.9 + - - +
161A ILE* 1.3 78.1 - - - +
163A VAL* 1.3 67.6 + - - +
164A LEU* 5.0 1.9 - - - +
199A SER* 3.9 24.3 + - - -
203A GLU* 4.0 23.5 + - + +
204A LEU 3.5 15.7 + - - +
205A SER* 3.3 10.6 - - - -
206A ILE* 3.1 26.9 + - - +
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Residues in contact with VAL 163 (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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139A ILE* 4.9 1.3 - - + -
150A ARG 3.3 1.4 - - - +
151A PHE* 3.3 8.7 - - - +
152A PHE* 2.9 65.0 + - + +
154A LEU* 3.5 33.4 - - + +
162A GLN* 1.3 76.6 - - - +
164A LEU* 1.3 61.3 + - - +
165A ALA* 4.7 0.7 - - + +
181A TYR* 5.4 1.1 - - + -
192A ILE* 3.8 22.9 - - + -
206A ILE* 3.6 9.9 - - + +
208A PRO* 4.0 26.2 - - + -
211A THR* 5.6 0.4 - - + +
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Residues in contact with LEU 164 (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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149A LEU* 4.5 10.3 - - + -
150A ARG 3.7 2.0 - - - +
151A PHE* 3.5 32.5 - - + -
162A GLN* 4.0 3.2 - - - +
163A VAL* 1.3 71.2 - - - +
165A ALA* 1.3 72.3 + - - +
166A ASN* 3.8 15.2 + - - +
199A SER* 3.8 20.2 - - - +
200A LYS* 4.1 17.3 - - + +
205A SER* 4.2 10.1 - - - +
206A ILE 3.0 7.3 + - - -
207A PHE* 3.2 65.0 - - + +
208A PRO* 3.2 2.6 - - - +
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Residues in contact with ALA 165 (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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149A LEU* 3.3 9.4 - - - +
150A ARG* 2.9 41.9 + - + +
152A PHE* 4.8 1.8 - - + -
163A VAL* 3.9 1.1 + - + -
164A LEU* 1.3 74.2 - - - +
166A ASN* 1.3 60.5 - - - +
177A PHE* 4.0 11.0 - - + -
181A TYR* 3.5 42.4 - - + +
208A PRO* 4.1 9.2 - - + +
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Residues in contact with ASN 166 (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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148A LYS* 4.0 6.9 - - - +
149A LEU* 4.6 13.4 - - - +
164A LEU* 3.8 12.4 + - + +
165A ALA* 1.3 74.7 - - - +
167A TYR* 1.3 73.5 + - - +
168A SER* 3.2 13.2 + - - -
169A PHE* 3.4 45.0 + - + +
170A HIS* 3.4 19.6 + - - +
177A PHE* 4.2 4.3 - - - -
200A LYS* 4.0 20.6 - - - +
208A PRO 5.0 4.0 + - - +
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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