Contacts of the strand formed by residues 101 - 108 (chain A) in PDB entry 1VLP
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 ILE 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 4.1 19.7 - - + -
60A LEU* 4.7 1.3 - - + -
97A PRO* 2.9 38.6 + - + +
98A GLU 4.3 7.4 - - - +
99A GLU 4.9 1.5 - - - +
100A GLN* 1.3 73.4 - - + +
102A SER* 1.3 62.0 - - - +
103A PHE* 3.9 24.3 + - + -
119A ILE* 4.0 18.6 - - + -
120A LEU 3.5 3.1 - - - +
121A VAL* 4.5 7.9 - - + -
131A TYR* 3.7 36.1 - - + -
135A LEU* 4.0 18.6 - - + -
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Residues in contact with SER 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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100A GLN 3.8 0.8 + - - -
101A ILE* 1.3 73.8 - - - +
103A PHE* 1.3 57.1 + - - +
104A THR* 4.1 10.3 + - - +
118A LYS* 3.5 3.3 - - - +
119A ILE* 3.3 4.5 - - - -
120A LEU* 2.8 50.1 + - - +
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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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50A ILE* 3.9 24.2 - - + -
53A LEU* 3.9 30.3 - - + -
54A LYS* 3.9 20.2 - - + -
57A PHE* 3.5 26.9 - + + -
101A ILE* 3.8 19.2 + - + -
102A SER* 1.3 72.5 + - - +
104A THR* 1.3 81.9 + - - +
105A SER* 5.1 0.2 - - - -
117A LEU* 4.0 19.5 - - + -
118A LYS 3.3 1.8 - - - -
119A ILE* 3.4 25.6 - - + -
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Residues in contact with THR 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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50A ILE* 6.2 0.2 - - - -
102A SER* 4.1 10.9 + - - +
103A PHE* 1.3 90.1 - - - +
105A SER* 1.3 67.6 + - - +
118A LYS* 2.8 55.9 + - - +
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Residues in contact with SER 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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50A ILE* 3.6 42.6 - - - +
103A PHE* 5.1 0.4 - - - -
104A THR* 1.3 81.4 - - - +
106A GLU* 1.3 60.7 + - - +
115A TYR* 4.0 10.4 - - - -
116A LYS 3.2 12.3 - - - -
117A LEU* 4.5 3.6 - - - -
118A LYS* 4.6 2.0 - - - +
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Residues in contact with GLU 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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105A SER* 1.3 76.0 - - - +
107A GLU* 1.3 74.3 + - - +
108A ILE 3.4 0.3 + - - -
115A TYR* 3.2 4.8 - - - -
116A LYS* 2.9 50.9 + - + +
118A LYS* 6.4 1.6 - - + -
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Residues in contact with GLU 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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106A GLU* 1.3 83.5 - - - +
108A ILE* 1.3 67.6 + - - +
109A GLU* 3.5 5.9 + - - +
112A PRO* 3.3 16.2 - - + +
113A THR* 2.7 31.5 + - - +
114A HIS 3.4 12.8 - - - +
115A TYR* 3.4 29.9 + - + -
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Residues in contact with ILE 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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41A SER 5.4 2.7 - - - +
44A THR* 3.4 35.2 - - + -
106A GLU 4.1 0.9 - - - +
107A GLU* 1.3 74.0 - - - +
109A GLU* 1.3 72.6 + - - +
110A GLY 3.2 0.5 + - - -
111A LYS* 2.8 50.2 + - + -
112A PRO* 3.9 2.1 - - - +
114A HIS* 2.8 15.7 + - + +
115A TYR 3.7 20.0 - - - +
116A LYS* 3.7 27.8 - - + +
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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