Contacts of the strand formed by residues 108 - 115 (chain A) in PDB entry 1PVI
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 ALA 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A TYR* 3.3 2.4 - - - -
105A ARG* 2.7 48.4 + - + +
107A ILE* 1.3 78.6 - - - +
109A ILE* 1.3 62.7 + - - +
13B TRP* 4.9 9.6 - - - +
17B GLN* 4.6 11.2 + - - +
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Residues in contact with ILE 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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41A GLN* 3.5 27.5 - - - +
42A VAL* 4.6 7.4 - - + -
45A ILE* 4.0 16.4 - - + -
102A ALA* 4.7 1.8 - - + -
103A ILE 4.1 5.6 - - - +
104A TYR* 3.7 31.6 - - + +
107A ILE 3.7 3.4 + - - -
108A ALA* 1.3 72.2 - - - +
110A GLU* 1.3 63.8 + - - +
111A ALA 4.4 8.7 - - - +
112A ILE* 3.9 31.2 - - + -
157A TYR* 4.2 23.3 + - + +
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Residues in contact with GLU 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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74A ILE* 3.2 28.6 - - - +
103A ILE* 2.8 23.3 + - + +
105A ARG* 4.8 13.1 - - + +
108A ALA 3.6 3.1 + - - +
109A ILE* 1.3 74.8 - - - +
111A ALA* 1.3 64.8 + - + +
150A MET* 5.9 3.1 - - - +
155A LYS* 4.7 3.2 + - - +
157A TYR* 4.0 17.3 - - - +
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Residues in contact with ALA 111 (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 ALA* 3.4 2.4 - - - +
103A ILE* 2.8 42.8 + - + +
109A ILE* 4.4 2.0 - - - +
110A GLU* 1.3 85.9 - - + +
112A ILE* 1.3 63.8 + - - +
113A TYR* 3.9 19.3 - - + -
155A LYS* 3.5 17.7 - - - +
157A TYR* 3.2 16.6 - - - +
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Residues in contact with ILE 112 (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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42A VAL* 4.2 12.1 - - + -
45A ILE* 4.6 11.4 - - + -
46A THR* 4.0 19.7 - - + -
100A ILE* 3.8 28.0 - - + -
101A PHE 3.5 5.6 - - - +
102A ALA* 4.3 6.3 - - + -
109A ILE* 3.9 26.0 - - + -
111A ALA* 1.3 76.9 - - - +
113A TYR* 1.3 57.0 + - - +
155A LYS* 3.8 1.2 - - - -
156A ILE* 2.8 48.8 + - + +
157A TYR* 2.9 32.0 + - + +
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Residues in contact with TYR 113 (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 ILE* 3.8 1.6 - - - -
101A PHE* 2.8 41.8 + - - +
103A ILE* 4.3 14.4 - - + -
111A ALA* 3.9 22.7 - - + -
112A ILE* 1.3 80.1 - - - +
114A ARG* 1.3 61.4 + - - +
149A VAL* 3.9 31.2 - - + +
150A MET* 3.5 51.9 + - + +
153A GLY 4.0 1.6 - - - -
154A THR 3.8 9.2 - - - +
155A LYS* 3.4 49.7 + - + +
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Residues in contact with ARG 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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67A TYR* 3.3 36.1 + - + -
98A PRO* 4.8 5.5 - - + +
99A TRP 3.6 5.2 - - - +
100A ILE* 4.0 22.9 - - + +
112A ILE 4.3 0.4 + - - -
113A TYR* 1.3 71.7 - - - +
115A LEU* 1.3 66.1 + - - +
116A GLU* 3.5 24.9 + - - +
153A GLY* 3.4 3.5 - - - -
154A THR* 3.0 46.5 + - + +
156A ILE* 4.4 26.9 - - + +
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Residues in contact with LEU 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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98A PRO* 3.4 6.1 - - - +
99A TRP 2.9 31.9 + - - -
101A PHE* 3.7 28.9 - - + -
114A ARG* 1.3 73.0 - - - +
116A GLU* 1.3 65.1 + - - +
119A ASP* 3.1 42.4 - - + +
120A LEU* 3.5 30.5 - - + +
148A TYR* 4.8 10.5 - - + -
149A VAL* 4.4 20.0 - - + +
152A HIS* 3.8 3.4 - - + +
153A GLY* 3.7 25.1 - - - +
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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