Contacts of the helix formed by residues 99 - 107 (chain A) in PDB entry 1RJV
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.1 6.7 - - - -
57A GLY 4.9 5.4 - - - -
58A PHE* 5.5 4.0 - - - -
97A LYS 3.5 0.2 + - - -
98A ILE* 1.3 72.8 - - - +
100A VAL* 1.3 60.0 + - - -
101A ASP 3.5 2.2 - - - -
102A GLU* 3.0 28.2 + - - +
103A PHE* 2.9 28.0 + - - +
111A CA 4.3 0.4 - - - -
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Residues in contact with VAL 100 (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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44A VAL* 3.1 43.7 - - + +
45A LYS* 4.0 20.6 - - + +
48A PHE* 3.6 34.5 - - + -
99A GLY* 1.3 70.1 - - - -
101A ASP* 1.3 68.6 + - + +
103A PHE* 3.1 4.5 + - - +
104A SER* 2.9 29.5 + - - -
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Residues in contact with ASP 101 (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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44A VAL* 5.5 0.7 - - - -
99A GLY 3.5 0.4 - - - -
100A VAL* 1.3 80.8 - - + +
102A GLU* 1.3 57.6 + - + +
104A SER* 3.6 6.3 - - - -
105A THR* 2.7 41.7 + - - +
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Residues in contact with GLU 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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90A GLY 3.8 13.5 - - - +
91A ASP 3.5 0.2 - - - -
92A LYS* 2.7 44.4 + - + +
93A ASP* 2.8 30.0 + - - +
97A LYS 3.4 1.0 - - - +
99A GLY* 3.0 27.3 + - - +
101A ASP* 1.3 76.9 - - + +
103A PHE* 1.3 54.3 + - - +
105A THR* 2.9 9.7 + - - -
106A LEU* 2.7 36.1 + - - +
111A CA 2.2 29.4 - - - -
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Residues in contact with PHE 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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19A PHE* 5.9 0.9 - + - -
25A PHE* 5.2 6.7 - + - -
27A HIS* 5.0 6.5 - - + -
31A PHE* 3.5 41.2 - + + -
47A VAL* 5.5 2.9 - - + -
48A PHE* 4.9 10.3 - + + -
51A LEU* 4.1 28.5 - - + -
59A ILE* 4.9 2.9 - - + -
67A ILE* 4.9 9.4 - - + -
71A PHE* 4.6 8.3 - + - -
86A LEU* 4.9 9.0 - - + -
90A GLY* 4.9 2.0 + - - -
98A ILE* 3.4 42.0 - - + -
99A GLY 2.9 19.4 + - - +
100A VAL* 3.1 6.0 + - - +
102A GLU* 1.3 73.0 - - - +
104A SER* 1.3 60.3 + - - +
105A THR 3.3 1.0 + - - -
106A LEU* 3.9 19.0 - - + +
107A VAL* 3.5 20.8 + - - +
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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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31A PHE* 4.2 10.9 - - - -
37A LYS* 4.0 13.5 - - - +
41A ALA* 5.7 1.6 - - - -
44A VAL* 3.7 32.0 - - - +
100A VAL 2.9 16.5 + - - -
101A ASP* 3.6 11.7 - - - -
103A PHE* 1.3 75.5 - - - +
105A THR* 1.3 63.5 + - - +
107A VAL* 3.3 14.9 - - - +
108A ALA* 4.3 1.4 - - - +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LYS* 5.7 1.9 - - - +
101A ASP* 2.7 29.5 + - - +
102A GLU* 2.9 12.6 + - - -
104A SER* 1.3 81.0 - - - +
106A LEU* 1.3 58.6 + - - +
107A VAL 3.1 1.3 - - - -
108A ALA* 2.9 29.6 + - + +
109A GLU* 3.1 15.7 + - - +
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Residues in contact with LEU 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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27A HIS* 3.4 35.6 + - + +
28A LYS* 4.3 6.1 - - - +
86A LEU* 5.9 1.1 - - + -
89A ALA* 3.1 32.5 - - + +
90A GLY* 4.1 12.6 - - - +
92A LYS* 3.9 31.0 - - + +
102A GLU 2.7 25.4 + - - +
103A PHE* 3.9 17.9 - - + +
105A THR* 1.3 69.9 + - - +
107A VAL* 1.3 66.3 + - + +
109A GLU* 3.6 15.1 - - - +
110A SER 4.3 1.2 + - - -
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Residues in contact with VAL 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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27A HIS* 3.3 32.1 - - + +
28A LYS* 3.7 10.4 - - - +
31A PHE* 3.2 48.7 - - + -
32A GLN* 4.0 2.4 + - - -
37A LYS* 2.8 28.0 + - + -
103A PHE 3.5 6.1 - - - +
104A SER 3.3 18.4 - - - +
106A LEU* 1.3 90.7 - - + +
108A ALA* 1.3 54.9 + - - +
109A GLU 3.3 1.6 - - - -
110A SER* 3.1 17.3 + - - -
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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