Contacts of the strand formed by residues 98 - 105 (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 PRO 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A GLN* 3.5 17.5 - - - +
66A GLU 3.3 20.4 - - - +
67A TYR* 3.4 30.7 - - + -
68A GLU 3.0 20.8 + - - -
96A GLN 4.4 2.5 - - - +
97A VAL* 1.3 89.9 - - - +
99A TRP* 1.3 61.9 + - + +
114A ARG* 4.8 9.0 - - + +
115A LEU 3.4 14.4 - - - +
116A GLU* 4.8 12.6 - - - +
117A PRO* 4.5 9.4 - - + -
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Residues in contact with TRP 99 (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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68A GLU* 3.2 27.8 - - + +
70A LYS* 3.8 36.6 - - + -
82A THR* 4.9 11.0 - - + -
86A MET* 6.5 0.2 - - + -
94A TYR* 3.4 27.8 + - + +
97A VAL 3.2 20.0 + - - -
98A PRO* 1.3 77.2 - - - +
100A ILE* 1.3 65.5 + - - +
101A PHE* 3.5 31.7 - + + -
113A TYR 4.0 0.5 - - - +
114A ARG* 3.6 3.5 - - - +
115A LEU 2.9 31.5 + - - +
120A LEU* 3.3 17.5 - - + -
124A TYR* 3.0 34.7 + + - -
127A TRP* 5.6 3.1 - + - -
144A ILE* 4.3 20.4 - - + -
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Residues in contact with ILE 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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42A VAL* 4.7 11.0 - - + -
46A THR* 5.6 1.3 - - + -
48A LEU* 4.3 13.2 - - + -
67A TYR* 3.8 37.9 - - + -
68A GLU 2.7 6.9 + - - +
69A LEU* 3.3 22.4 - - + +
70A LYS* 3.0 24.8 + - - +
99A TRP* 1.3 80.5 - - - +
101A PHE* 1.3 66.0 + - - +
102A ALA 4.2 0.7 - - - +
112A ILE* 3.8 24.9 - - + -
113A TYR 3.8 2.0 - - - +
114A ARG* 4.0 22.2 - - + +
156A ILE* 4.7 10.8 - - + -
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Residues in contact with PHE 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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70A LYS* 3.5 13.0 - - + -
80A PHE* 3.5 44.0 - + + -
99A TRP* 3.5 45.5 - + + -
100A ILE* 1.3 79.8 - - - +
102A ALA* 1.3 59.6 + - - +
103A ILE* 4.6 2.2 - - + +
111A ALA 4.0 0.7 - - - +
112A ILE* 3.5 1.5 - - - -
113A TYR* 2.8 47.2 + - - +
115A LEU* 3.7 31.6 - - + -
120A LEU* 4.2 9.0 - - + -
144A ILE* 4.2 16.6 - - + -
149A VAL* 3.9 24.7 - - + -
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Residues in contact with ALA 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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42A VAL* 4.0 24.0 - - + -
70A LYS 3.1 11.1 + - - +
71A SER* 3.4 5.1 - - - +
72A ILE 3.0 23.9 + - - -
80A PHE* 3.9 3.8 - - - -
100A ILE* 4.2 0.8 - - + -
101A PHE* 1.3 73.6 - - - +
103A ILE* 1.3 62.8 + - - +
104A TYR* 3.8 20.7 - - + +
109A ILE* 4.7 2.2 - - + -
111A ALA 3.4 7.0 - - - +
112A ILE* 4.3 11.7 - - + +
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Residues in contact with ILE 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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72A ILE* 3.6 18.8 - - + -
74A ILE* 3.9 31.4 - - + -
80A PHE* 4.4 10.8 - - + -
101A PHE 4.6 3.4 - - - +
102A ALA* 1.3 77.1 - - - +
104A TYR* 1.3 57.4 + - - +
109A ILE* 3.8 1.9 - - - +
110A GLU* 2.8 39.3 + - + +
111A ALA* 2.8 25.3 + - + +
113A TYR* 4.3 24.9 - - + -
146A VAL* 4.0 21.3 - - + +
149A VAL* 6.0 3.1 - - + -
150A MET* 4.5 9.4 - - + -
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Residues in contact with TYR 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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38A LYS* 2.8 58.6 + - + +
41A GLN* 3.4 20.9 - - - -
42A VAL* 3.0 17.3 - - + +
71A SER* 3.9 14.3 + - - -
72A ILE 2.8 23.2 + - - +
73A ASN* 3.3 2.5 - - - -
74A ILE* 2.8 33.7 + - - +
102A ALA* 3.8 22.4 - - + -
103A ILE* 1.3 76.0 - - - +
105A ARG* 1.3 59.8 + - - +
106A GLY 3.1 20.2 + - - +
107A ILE 4.0 9.6 - - - -
108A ALA 3.3 5.4 - - - +
109A ILE* 3.7 27.4 - - + -
110A GLU* 5.2 0.2 - - - -
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Residues in contact with ARG 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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74A ILE* 4.3 6.3 - - + +
75A ASP* 3.7 25.5 + - - +
103A ILE 4.3 0.4 + - - -
104A TYR* 1.3 69.7 - - - +
106A GLY* 1.3 58.0 + - - +
107A ILE 2.8 9.7 + - - -
108A ALA* 2.7 28.5 + - + +
110A GLU* 4.8 15.9 - - + +
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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