Contacts of the helix formed by residues 102 - 110 (chain A) in PDB entry 4J6V
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 ASP 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 3.5 10.0 - - - +
101A GLN* 1.3 83.6 - - + +
103A PRO* 1.3 68.1 - - - +
104A SER* 2.7 34.5 + - - -
105A GLN* 3.0 38.8 + - + +
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Residues in contact with PRO 103 (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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97A ASP* 3.5 29.2 - - + +
98A ALA* 4.7 4.9 - - - +
100A MET* 4.0 11.9 - - + +
101A GLN 3.9 6.5 - - - +
102A ASP* 1.3 90.7 - - - +
104A SER* 1.3 54.6 + - - +
105A GLN 3.0 0.9 - - - -
106A SER* 3.0 28.9 + - - -
109A TRP* 3.8 6.3 + - - -
161A THR* 6.6 0.2 - - - -
162A LEU* 4.0 25.8 - - + +
210A TRP* 4.0 16.2 - - + +
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Residues in contact with SER 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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102A ASP* 2.7 33.4 + - - -
103A PRO* 1.3 77.2 - - - +
105A GLN* 1.3 68.2 + - - +
106A SER 3.3 1.5 - - - +
109A TRP* 3.5 27.3 - - - +
117A ASN* 5.3 5.6 - - - -
153A PHE* 3.7 28.9 - - - -
210A TRP* 4.7 3.1 - - - -
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Residues in contact with GLN 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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100A MET* 3.8 13.0 - - + +
102A ASP* 3.3 31.3 + - + +
103A PRO 3.0 1.4 - - - -
104A SER* 1.3 98.8 + - - +
106A SER* 1.3 66.9 + - - +
107A GLN* 3.5 3.6 + - - +
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Residues in contact with SER 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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12A LEU* 4.3 7.3 - - - +
97A ASP* 2.6 39.1 + - - -
100A MET* 3.8 13.5 - - - +
103A PRO 3.0 15.0 + - - -
104A SER 3.3 0.4 - - - -
105A GLN* 1.3 81.3 - - - +
107A GLN* 1.3 63.8 + - - +
108A ILE* 3.0 21.9 + - - +
109A TRP* 3.2 18.6 + - - +
110A SER* 5.2 0.2 - - - -
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Residues in contact with GLN 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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11A VAL* 5.5 0.7 - - - -
12A LEU* 4.0 25.2 - - + +
19A LYS* 4.6 23.4 + - - +
105A GLN 3.5 3.3 + - - +
106A SER* 1.3 74.9 + - - +
108A ILE* 1.3 57.8 + - - +
109A TRP 3.1 0.2 - - - -
110A SER* 3.0 33.8 + - - +
113A PHE* 4.5 1.4 - - - +
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Residues in contact with ILE 108 (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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11A VAL* 4.3 15.5 - - + -
12A LEU* 4.5 3.7 - - + +
92A TRP* 3.2 50.0 - - + +
97A ASP* 4.0 5.2 - - - +
106A SER* 3.0 20.4 + - - +
107A GLN* 1.3 80.3 - - - +
109A TRP* 1.3 86.1 + - + +
110A SER 3.2 3.4 + - - -
113A PHE* 3.5 13.8 - - + -
114A MET* 3.2 36.0 + - + +
226A VAL* 4.1 13.7 - - + -
229A LEU* 4.2 8.3 - - + -
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Residues in contact with TRP 109 (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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92A TRP* 3.7 30.8 - + - -
103A PRO 3.8 16.4 + - - -
104A SER* 3.5 27.5 - - - +
106A SER* 3.2 9.9 + - - +
107A GLN 3.1 1.0 - - - -
108A ILE* 1.3 98.1 - - + +
110A SER* 1.3 62.5 + - - +
111A ALA 3.9 0.5 + - - -
114A MET* 4.0 7.4 - - + -
115A GLY 3.1 43.0 - - - +
116A GLY* 3.8 10.0 + - - -
151A ARG* 3.7 25.1 - - - -
153A PHE* 3.5 37.4 - + + -
210A TRP* 4.0 8.8 - + - -
211A VAL* 4.4 4.9 - - + -
226A VAL* 3.8 33.9 - - + -
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Residues in contact with SER 110 (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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19A LYS* 4.5 2.9 - - - -
107A GLN* 3.0 25.1 + - - +
108A ILE 3.2 1.6 - - - -
109A TRP* 1.3 77.7 - - - +
111A ALA* 1.3 57.5 + - - +
112A ASP* 2.5 29.4 + - - -
113A PHE* 2.9 24.8 + - - +
115A GLY 2.9 20.0 + - - -
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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