Contacts of the helix formed by residues 102 - 110 (chain A) in PDB entry 4P7A
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 GLU 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 6.1 3.6 - - + -
79A ARG* 3.1 38.0 + - + +
80A PHE* 4.0 12.9 - - + -
98A GLY* 4.6 3.9 + - - +
99A PHE* 3.2 47.2 + - - +
100A ARG 4.2 1.6 - - - +
101A GLY* 1.3 80.5 - - - +
103A ALA* 1.3 60.7 + - - +
104A LEU 3.6 0.7 - - - -
105A ALA* 3.8 6.3 - - - +
106A SER* 2.9 40.5 + - - +
402A ADP 4.8 0.2 + - - -
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Residues in contact with ALA 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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24A VAL* 5.9 3.6 - - - -
25A ILE* 4.5 2.2 - - - +
34A GLU* 3.6 41.5 - - + +
38A ASN* 5.0 2.0 - - - +
102A GLU* 1.3 77.4 - - - +
104A LEU* 1.3 64.4 + - + +
106A SER* 3.2 6.1 + - - -
107A ILE* 3.0 29.0 + - + +
401A MG 4.3 0.7 - - - -
402A ADP 3.4 19.9 + - - +
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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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35A MET* 4.7 10.1 - - + -
38A ASN* 4.3 9.2 - - - +
76A VAL* 4.2 14.1 - - + +
77A CYS* 4.2 24.4 - - - +
103A ALA* 1.3 74.8 - - + +
105A ALA* 1.3 62.9 + - - +
107A ILE* 3.8 21.7 - - + +
108A SER* 2.9 26.2 + - - -
113A VAL* 5.3 5.2 - - + +
115A ILE* 4.7 8.1 - - + -
150A ILE* 4.7 21.5 - - + -
402A ADP 2.9 57.6 + - + +
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Residues in contact with ALA 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 CYS 3.0 26.2 + - - +
78A GLU 3.7 5.1 + - - +
79A ARG* 3.7 34.1 - - + +
101A GLY 4.2 3.1 - - - +
102A GLU 3.6 8.2 + - - +
103A ALA 3.2 0.4 - - - -
104A LEU* 1.3 79.4 - - - +
106A SER* 1.3 62.5 + - - +
108A SER* 3.3 7.5 + - - -
109A HIS* 2.8 29.5 + - + +
402A ADP 4.4 1.4 + - - -
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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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21A ALA* 3.3 34.0 - - - +
24A VAL* 4.2 19.1 - - - +
25A ILE* 4.1 17.7 - - - -
102A GLU* 2.9 27.1 + - - +
103A ALA 3.2 3.8 + - - -
105A ALA* 1.3 73.6 - - - +
107A ILE* 1.3 67.3 + - - +
109A HIS* 3.0 12.9 + - - +
110A VAL* 3.5 4.7 + - - +
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Residues in contact with ILE 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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25A ILE* 3.4 21.1 - - + -
31A ALA* 4.1 32.8 - - + +
34A GLU* 4.8 6.5 - - + -
35A MET* 4.3 15.7 - - + -
103A ALA* 3.0 18.3 + - + +
104A LEU* 3.8 16.4 - - + +
106A SER* 1.3 75.4 - - - +
108A SER* 1.3 57.5 - - - +
110A VAL* 3.2 10.3 + - - +
111A ALA* 3.1 25.9 + - + +
113A VAL* 3.8 18.6 - - + -
152A VAL* 3.8 26.9 - - + -
155A LEU* 5.3 2.2 - - + -
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Residues in contact with SER 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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77A CYS* 4.2 8.3 - - - -
104A LEU 2.9 18.4 + - - -
105A ALA 3.6 5.2 - - - -
106A SER 3.1 0.2 - - - -
107A ILE* 1.3 76.8 - - - +
109A HIS* 1.3 58.3 + - - +
110A VAL 3.3 0.2 - - - -
111A ALA 3.4 6.1 - - - +
113A VAL* 3.8 9.8 - - - +
130A TYR* 3.6 8.8 - - - +
132A ASP* 3.0 16.9 + - - +
133A GLY* 2.9 27.5 + - - -
157A TYR* 5.6 1.2 + - - -
409A UNX 3.0 27.3 - - - -
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Residues in contact with HIS 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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14A THR* 5.3 3.4 - - - -
17A ASN* 3.7 41.2 + - + +
18A ARG* 4.0 9.0 - - - +
21A ALA* 3.8 13.2 - - + -
78A GLU* 6.5 0.2 - - - -
79A ARG* 6.2 3.6 - - + -
105A ALA* 2.8 29.4 + - + -
106A SER* 3.0 11.3 + - - +
108A SER* 1.3 78.9 - - - +
110A VAL* 1.3 55.7 + - - +
111A ALA 3.8 0.7 - - - -
132A ASP* 3.6 50.6 + - + +
133A GLY* 4.2 4.0 - - - -
157A TYR* 5.7 0.2 - - - -
158A ASN* 2.7 27.6 + - - -
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Residues in contact with VAL 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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18A ARG* 3.7 13.0 - - + +
21A ALA* 4.0 3.8 - - + +
22A GLY 3.9 8.1 - - - +
25A ILE* 4.6 9.4 - - + -
106A SER 3.7 8.3 - - - +
107A ILE* 3.2 12.3 + - - +
109A HIS* 1.3 85.7 - - - +
111A ALA* 1.3 57.1 + - - +
154A ASP 3.8 0.9 - - - +
155A LEU* 3.5 9.3 - - + -
156A PHE* 2.7 56.9 + - + -
157A TYR* 4.1 6.5 - - - -
158A ASN* 3.6 7.6 - - - +
159A ILE* 3.3 30.1 - - + -
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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