Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 2JI8
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.4 16.4 - - - -
94A ALA* 4.5 2.0 - - - -
95A THR* 3.2 18.9 + - - +
99A PHE 3.8 1.6 + - - -
101A MET* 3.1 13.2 - - - -
133A CYS* 3.1 7.0 - - - +
134A LYS* 2.9 28.1 + - - +
162A GLY* 1.3 72.9 - - - -
164A VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 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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91A LEU* 3.7 4.6 - - - +
101A MET 2.8 10.0 + - - +
102A ILE* 3.3 7.6 - - + +
103A LEU 2.9 24.8 + - - +
135A ALA 3.5 12.8 - - - +
137A PHE* 3.7 30.1 - - + -
152A ALA* 3.5 35.0 - - + +
155A THR* 3.7 15.7 - - + -
156A ALA* 3.5 22.4 - - + +
162A GLY 4.2 0.2 - - - +
163A GLY* 1.3 77.9 - - - +
165A TYR* 1.3 66.0 + - - +
166A VAL* 4.4 0.4 - - + -
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Residues in contact with TYR 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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84A PHE* 3.6 13.5 - + - -
91A LEU* 4.0 11.0 - - + +
103A LEU* 3.2 21.5 - - + -
105A SER* 3.5 28.2 + - - -
125A GLN* 3.0 23.4 + - - -
126A MET* 3.5 22.0 - - - -
129A ALA* 3.7 25.6 - - + -
133A CYS* 4.1 3.1 - - - -
135A ALA 3.1 8.0 + - - +
136A SER* 3.5 22.3 - - - +
137A PHE 2.7 32.0 + - - -
164A VAL* 1.3 73.9 - - - +
166A VAL* 1.3 67.3 + - - +
167A ASP* 2.7 38.0 + - + -
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Residues in contact with VAL 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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102A ILE* 4.0 12.3 - - + -
103A LEU 3.0 8.5 + - - +
104A LEU* 3.5 24.5 - - + -
105A SER 3.3 22.5 + - - -
137A PHE* 3.7 13.2 - - + +
139A ILE* 3.6 33.9 - - + +
148A GLY 4.9 2.5 - - - +
149A ILE* 4.9 2.0 - - + -
152A ALA* 3.7 30.1 - - + -
164A VAL* 4.4 2.7 - - + -
165A TYR* 1.3 79.3 - - - +
167A ASP* 1.3 67.9 + - - +
168A LEU* 3.7 5.2 + - + +
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Residues in contact with ASP 167 (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 SER 3.7 0.2 - - - -
107A SER* 2.5 36.0 + - - -
125A GLN* 3.5 12.5 + - - +
126A MET* 3.9 4.4 + - + -
137A PHE 2.9 18.8 + - - +
138A ARG* 3.3 32.0 + - + +
139A ILE 3.2 24.1 + - - -
165A TYR* 2.7 32.7 + - + -
166A VAL* 1.3 72.3 - - - +
168A LEU* 1.3 62.6 + - - +
169A PRO* 3.4 5.7 - - - +
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Residues in contact with LEU 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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16A LEU* 3.7 29.6 - - + -
39A LEU* 4.7 5.2 - - + -
77A LEU* 4.9 2.9 - - + -
104A LEU* 3.8 29.8 - - + -
105A SER 2.9 17.0 + - - +
106A GLY* 3.3 4.7 - - - -
107A SER* 3.1 17.7 + - - -
139A ILE* 4.2 10.3 - - + -
166A VAL* 4.0 19.7 - - + +
167A ASP* 1.3 80.1 + - - +
169A PRO* 1.3 70.0 - - - +
170A ALA 3.4 0.3 + - - -
172A LEU* 3.5 24.0 - - + -
173A PHE* 3.6 24.9 - - + -
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Residues in contact with PRO 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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107A SER* 3.2 13.6 - - - +
108A SER 4.4 7.0 - - - +
110A ARG* 5.0 7.2 - - + +
138A ARG* 3.8 17.9 - - + -
139A ILE 3.3 22.7 - - - +
140A ASN* 4.3 11.9 - - - +
167A ASP* 3.4 17.9 - - - +
168A LEU* 1.3 87.0 - - - +
170A ALA* 1.3 67.8 + - - +
171A LYS* 4.3 7.4 - - + +
172A LEU* 2.9 23.5 + - + +
173A PHE* 4.0 2.8 - - - -
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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