Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 6VSB
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.3 7.9 - - - -
106A PHE 3.0 12.6 - - - -
107A GLY* 3.5 7.6 - - - -
110A LEU* 3.3 32.2 + - - -
114A THR 3.2 9.8 + - - -
115A GLN* 1.3 79.8 + - - +
117A LEU* 1.3 63.1 + - - +
118A LEU* 3.3 13.6 + - - +
129A LYS 2.9 14.4 - - - +
130A VAL* 3.8 1.5 + - - -
131A CYS 3.2 16.0 + - - +
133A PHE* 3.8 6.7 - - - -
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Residues in contact with LEU 117 (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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104A TRP 3.5 2.8 - - - +
105A ILE* 3.6 0.2 - - - -
106A PHE* 2.8 35.3 + - + +
116A SER* 1.3 69.9 - - - +
118A LEU* 1.3 61.8 - - - +
119A ILE* 2.9 23.1 + - + +
128A ILE* 4.4 4.9 - - + -
129A LYS 3.2 6.5 - - - +
130A VAL* 3.7 23.1 - - + -
201A PHE* 4.4 20.2 - - + -
229A LEU* 4.2 15.3 - - + -
231A ILE* 3.7 49.6 - - + -
233A ILE* 4.3 12.1 - - + -
235A ILE* 4.7 7.0 - - + -
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Residues in contact with LEU 118 (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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104A TRP 3.7 6.1 - - - -
105A ILE* 3.8 36.8 - - + -
116A SER* 3.6 7.6 - - - +
117A LEU* 1.3 67.3 - - - +
119A ILE* 1.3 60.6 + - - +
120A VAL* 3.0 23.6 + - + +
127A VAL* 3.1 12.1 - - - +
128A ILE* 3.7 5.5 - - - -
129A LYS* 3.1 19.5 + - + +
133A PHE* 3.5 58.1 - - + -
159A VAL* 4.4 8.3 - - + +
160A TYR* 3.9 19.5 - - + +
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Residues in contact with ILE 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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103A GLY* 3.1 6.2 - - - -
104A TRP* 3.0 41.9 + - + +
106A PHE* 4.7 10.1 - - + -
117A LEU* 2.9 25.5 + - + +
118A LEU* 1.3 68.7 - - - +
120A VAL* 1.3 58.9 + - - +
126A VAL* 4.3 3.1 - - + -
127A VAL 3.8 3.6 - - - -
128A ILE* 4.1 30.1 - - + -
175A PHE* 3.9 29.6 - - + -
194A PHE* 5.7 2.0 - - + -
201A PHE* 3.6 34.8 - - + -
203A ILE* 4.1 13.5 - - + -
229A LEU* 5.6 0.7 - - + -
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Residues in contact with VAL 120 (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 ARG* 4.2 7.2 - - + +
103A GLY* 4.3 0.7 - - - -
118A LEU* 3.0 30.7 + - + +
119A ILE* 1.3 76.3 - - - +
121A ASN* 1.3 70.8 + - - +
122A ASN* 4.2 7.4 - - + +
126A VAL* 3.3 7.1 - - - +
127A VAL* 3.0 41.3 + - + +
141A LEU* 5.1 15.3 - - + -
157A PHE* 6.6 0.2 - - + -
159A VAL* 5.9 3.6 - - + -
175A PHE* 6.0 0.2 - - - -
241A LEU* 3.8 24.0 - - + -
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Residues in contact with ASN 121 (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 ARG* 3.2 42.5 + - - +
120A VAL* 1.3 80.2 - - - +
122A ASN* 1.3 58.0 + - - +
123A ALA* 3.3 9.3 + - - +
125A ASN 3.0 17.0 - - - +
126A VAL* 4.5 2.7 - - + -
141A LEU* 5.8 0.5 - - - +
174A PRO* 3.1 20.9 - - - +
175A PHE* 3.0 43.7 - - + +
176A LEU* 3.1 17.0 - - - +
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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