Contacts of the strand formed by residues 101 - 107 (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 MET 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLY* 3.7 35.9 - - - +
63A ALA* 4.0 6.3 - - + +
64A SER* 3.9 11.9 - - - -
73A PRO* 4.2 0.7 - - - -
74A GLY 3.4 15.3 - - - +
76A CYS* 4.0 16.2 - - + -
87A GLY 4.5 2.5 - - - +
90A SER* 4.5 0.7 - - - -
91A LEU* 3.8 33.2 - - + +
94A ALA* 3.6 32.1 - - + -
99A PHE 3.1 3.4 + - - -
100A PRO* 1.3 75.3 - - - +
102A ILE* 1.3 65.2 + - - +
103A LEU* 4.3 8.5 - - + -
156A ALA* 4.0 2.2 - - - +
162A GLY 3.2 5.7 + - - +
163A GLY* 3.1 3.6 - - - -
164A VAL* 2.8 31.5 + - - +
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Residues in contact with ILE 102 (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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20A LEU* 5.7 5.6 - - + -
25A ILE* 5.9 1.3 - - + -
73A PRO* 3.7 22.2 - - + -
74A GLY 2.9 9.3 + - - +
75A VAL* 3.5 15.7 - - + +
76A CYS 3.0 24.8 + - - +
101A MET* 1.3 81.9 - - - +
103A LEU* 1.3 67.1 + - - +
104A LEU* 3.8 13.6 + - + -
149A ILE* 5.7 4.3 - - + -
152A ALA* 3.8 31.2 - - + +
153A VAL* 4.0 19.7 - - + -
156A ALA* 4.5 1.1 - - + -
164A VAL* 3.3 10.1 - - + +
166A VAL* 4.0 22.7 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A CYS* 3.7 16.8 - - - -
78A THR* 3.7 24.5 - - + +
84A PHE* 4.2 6.7 - - + +
87A GLY* 3.7 7.4 - - - +
88A VAL* 3.5 40.4 - - + +
91A LEU* 4.0 30.0 - - + +
101A MET* 4.3 4.9 - - + -
102A ILE* 1.3 71.7 - - - +
104A LEU* 1.3 60.2 - - - +
105A SER* 3.4 21.8 - - - +
164A VAL 2.9 8.7 + - - +
165A TYR* 3.2 13.8 - - + -
166A VAL 3.0 25.6 + - - -
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Residues in contact with LEU 104 (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* 4.9 4.5 - - + -
20A LEU* 4.2 17.5 - - + -
28A MET* 4.1 14.8 - - + -
39A LEU* 5.5 0.4 - - + -
75A VAL* 3.6 25.8 - - + -
76A CYS 2.8 14.8 + - - +
77A LEU* 3.3 11.4 - - + +
78A THR 3.0 22.2 + - - -
102A ILE* 3.8 10.7 + - + -
103A LEU* 1.3 70.5 - - - +
105A SER* 1.3 64.9 + - - +
149A ILE* 4.3 15.5 - - + -
166A VAL* 3.5 32.5 - - + -
168A LEU* 3.8 26.9 - - + -
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Residues in contact with SER 105 (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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77A LEU* 5.1 0.2 - - - -
78A THR* 2.8 28.1 + - - -
79A VAL 3.8 7.2 - - - -
84A PHE* 3.8 5.9 - - - -
103A LEU* 3.4 13.5 - - - +
104A LEU* 1.3 75.9 + - - +
106A GLY* 1.3 61.6 + - - +
125A GLN* 3.9 5.8 - - - -
165A TYR* 3.5 29.0 + - - -
166A VAL 3.3 8.3 + - - -
168A LEU* 2.9 26.7 + - - +
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Residues in contact with GLY 106 (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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35A PRO* 4.0 10.5 - - - -
36A ILE* 3.6 23.6 - - - +
78A THR 3.1 12.3 + - - -
79A VAL 3.7 0.2 - - - -
80A SER* 3.2 18.3 + - - -
105A SER* 1.3 71.2 - - - +
107A SER* 1.3 58.5 + - - -
125A GLN* 3.1 18.0 + - - -
168A LEU* 3.3 12.7 - - - +
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Residues in contact with SER 107 (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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35A PRO* 4.1 5.0 - - - +
80A SER* 4.1 4.0 - - - -
106A GLY* 1.3 75.2 - - - -
108A SER* 1.3 65.2 + - - +
110A ARG* 4.9 5.6 + - - -
123A MET 5.4 3.4 - - - -
125A GLN* 3.8 14.8 - - - -
138A ARG* 6.0 0.9 - - - -
167A ASP* 2.5 39.4 + - - -
168A LEU 3.1 5.3 + - - -
169A PRO* 3.2 15.4 - - - +
170A ALA* 2.8 28.9 + - - +
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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