Contacts of the helix formed by residues 113 - 119 (chain A) in PDB entry 1PV7
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 TYR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 2.7 52.2 - + - -
59A PHE* 3.8 30.2 - + - -
83A MET* 4.1 15.5 - - + -
90A PHE* 6.0 1.1 - - + -
109A VAL* 3.7 12.2 - - + +
110A GLY* 5.0 7.4 - - - +
111A GLY 2.9 6.3 + - - -
112A ILE* 1.3 95.2 - - - +
114A LEU* 1.3 57.4 + - - +
115A GLY 2.6 4.6 - - - +
116A PHE* 2.6 44.1 + + + +
117A CYS* 3.1 0.7 - - - -
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Residues in contact with LEU 114 (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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26A TYR* 5.6 0.6 - - + -
83A MET* 3.0 43.5 - - + +
84A LEU* 4.6 4.8 - - + +
86A MET* 3.6 16.4 - - + +
87A PHE* 3.4 30.5 - - + -
90A PHE* 3.0 66.3 - - + -
91A PHE* 4.6 0.9 - - + -
111A GLY 3.9 1.8 + - - -
113A TYR* 1.3 77.7 - - - +
115A GLY* 1.3 58.3 + - - +
117A CYS* 3.1 31.1 - - - +
118A PHE* 5.1 3.7 - - + -
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Residues in contact with GLY 115 (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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26A TYR* 3.8 33.1 + - - -
52A ILE* 5.2 5.1 - - - +
90A PHE* 4.5 1.8 - - - -
91A PHE* 5.9 0.4 - - - -
95A PHE* 5.6 2.0 - - - -
111A GLY 3.5 13.5 + - - -
112A ILE* 4.3 9.4 - - - +
113A TYR 2.6 5.2 - - - +
114A LEU* 1.3 82.9 - - - +
116A PHE* 1.3 61.0 + - - -
117A CYS 3.6 0.2 + - - -
118A PHE* 3.9 7.3 + - - +
119A ASN* 4.7 3.8 + - - +
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Residues in contact with PHE 116 (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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55A PHE* 4.9 6.1 - - + +
59A PHE* 3.5 47.8 - + + -
63A PHE* 4.4 24.5 - + - -
76A LEU* 6.2 1.1 - - + -
79A ILE* 5.3 11.4 - - + -
80A ILE* 5.4 7.6 - - + -
83A MET* 4.1 14.4 - - - -
112A ILE* 4.2 8.7 - - - +
113A TYR* 2.6 41.5 + - + +
115A GLY* 1.3 69.8 - - - +
117A CYS* 1.3 71.1 + - - -
118A PHE 2.7 17.7 + - - -
119A ASN* 3.0 17.3 + - - +
120A ALA* 3.5 26.8 + - + +
121A GLY* 4.0 2.4 + - - -
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Residues in contact with CYS 117 (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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19A TYR* 2.7 26.3 + - - -
79A ILE 5.3 0.9 - - - -
80A ILE* 4.5 9.9 - - + +
83A MET* 3.7 20.9 - - - -
84A LEU* 3.4 25.8 - - + +
113A TYR 3.1 18.2 - - - -
114A LEU* 3.1 20.4 - - - +
115A GLY 3.2 0.4 - - - -
116A PHE* 1.3 99.8 - - - +
118A PHE* 1.3 57.2 + - - +
119A ASN 3.8 0.4 - - - -
121A GLY* 4.0 5.6 - - - +
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Residues in contact with PHE 118 (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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19A TYR* 3.6 33.9 - + - -
22A ILE* 3.1 51.6 - - + -
23A MET* 3.7 35.2 - - + +
26A TYR* 3.7 40.4 - + + -
84A LEU* 3.6 18.4 - - + -
87A PHE* 4.5 7.4 - + - -
114A LEU 5.1 4.9 - - - -
115A GLY 3.9 7.3 + - - +
116A PHE 2.7 3.6 + - - -
117A CYS* 1.3 86.9 - - - +
119A ASN* 1.3 58.1 + - - +
122A ALA* 4.1 13.3 - - - +
1E YIO 5.1 3.1 + - - -
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Residues in contact with ASN 119 (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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52A ILE* 4.8 12.7 - - + +
56A SER* 2.8 42.2 + - - +
60A GLN* 3.4 11.4 + - - -
115A GLY 4.7 2.4 + - - +
116A PHE* 3.0 10.4 + - - +
118A PHE* 1.3 79.0 - - - +
120A ALA* 1.3 56.5 + - - +
122A ALA* 3.6 2.9 - - - +
123A PRO* 2.7 33.3 - - - +
359A GLN* 4.9 3.4 + - - +
2E GAL 6.0 2.3 - - - -
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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