Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 3RJD
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 GLY 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ARG* 5.2 0.7 - - - -
140A ASN* 3.3 13.9 - - - -
162A HIS 3.8 0.4 + - - -
163A ASN* 1.3 78.5 - - - +
165A THR* 1.3 62.1 + - - -
166A TYR* 3.5 12.9 - - - -
182A SER* 4.4 2.2 - - - -
183A VAL 3.0 33.6 + - - +
1E NAG 3.9 14.6 - - - -
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Residues in contact with THR 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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138A TYR 3.9 0.2 - - - +
139A ARG* 3.6 2.8 - - - -
140A ASN* 2.8 50.1 + - - +
164A GLY* 1.3 71.4 - - - -
166A TYR* 1.3 60.2 + - - +
167A HIS* 3.6 23.3 + - + +
180A GLY* 4.2 2.1 - - - -
181A ILE 3.2 20.4 + - - -
182A SER* 4.3 9.9 - - - +
1E NAG 5.2 6.3 - - + -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.4 29.5 - - + +
120A LEU* 4.4 8.8 - - + +
122A LEU* 3.9 20.9 - - + -
137A TYR* 5.9 0.4 - + - -
138A TYR 3.3 17.5 - - - -
139A ARG* 3.3 25.9 + - + -
144A PHE* 3.7 28.9 - + - -
155A ILE* 4.3 4.1 - - + +
162A HIS* 2.6 40.6 + - - +
164A GLY 3.5 14.6 - - - -
165A THR* 1.3 73.5 - - - +
167A HIS* 1.3 60.5 + - - +
179A ALA 4.1 1.0 - - - +
180A GLY* 3.2 6.4 - - - -
181A ILE 2.8 30.2 + - - +
183A VAL* 3.6 28.5 - - + -
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Residues in contact with HIS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.4 11.7 - - - +
137A TYR* 3.7 0.9 - - - -
138A TYR* 2.9 47.4 + - + +
141A GLY* 5.1 9.6 - - - -
165A THR* 3.6 19.4 + - + +
166A TYR* 1.3 77.2 - - - +
168A CYS* 1.3 64.9 + - - +
177A THR* 6.5 0.4 - - - -
178A SER* 3.2 26.7 + - - +
179A ALA* 4.0 0.7 - - - -
180A GLY* 3.2 27.1 + - - -
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Residues in contact with CYS 168 (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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105A LEU* 3.9 2.9 - - - +
106A LEU 4.4 1.1 - - - -
107A LEU* 3.8 16.2 - - + -
124A CYS* 2.0 57.0 - - + -
136A LEU 3.2 12.6 - - - +
137A TYR* 4.2 3.8 - - + -
138A TYR* 4.0 3.8 - - - -
167A HIS* 1.3 76.8 - - - +
169A SER* 1.3 57.9 + - - +
177A THR* 3.6 2.6 - - - -
178A SER* 2.9 49.2 + - - -
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Residues in contact with SER 169 (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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105A LEU* 3.9 2.9 - - - -
124A CYS* 4.8 0.2 - - - -
135A VAL* 3.3 6.0 - - - +
136A LEU* 2.8 34.0 + - - +
138A TYR* 2.6 33.9 + - - -
168A CYS* 1.3 74.8 - - - +
170A GLY* 1.3 58.9 + - - +
175A ARG* 3.4 20.8 + - - -
176A TYR 3.3 14.8 - - - -
177A THR* 4.0 12.6 - - - -
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Residues in contact with GLY 170 (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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105A LEU* 3.4 10.5 - - - +
132A VAL* 4.7 7.0 - - - -
133A TYR 3.8 6.7 - - - -
134A ASN 3.9 5.2 - - - -
135A VAL* 4.2 10.1 - - - -
169A SER* 1.3 76.1 - - - +
171A MET* 1.3 61.7 + - - -
172A GLY 3.8 0.3 + - - -
174A HIS 3.8 0.7 - - - +
175A ARG* 3.6 8.3 - - - +
176A TYR* 3.0 33.4 + - - +
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Residues in contact with MET 171 (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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132A VAL* 3.5 4.4 - - - -
133A TYR* 2.8 88.4 + - + +
134A ASN* 4.2 10.5 + - + +
170A GLY* 1.3 70.3 - - - -
172A GLY* 1.3 62.2 + - - +
173A LYS 5.1 1.1 - - - +
174A HIS* 3.8 9.4 - - - -
175A ARG* 3.7 39.9 - - + +
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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