Contacts of the strand formed by residues 124 - 130 (chain A) in PDB entry 1VCA
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 LEU 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.2 15.5 - - + -
115A VAL* 4.4 4.0 - - + -
118A VAL* 4.2 22.4 - - + -
120A PRO 3.9 0.2 + - - -
121A PHE* 3.0 14.9 + - - +
122A ASP 4.9 1.0 - - - +
123A ARG* 1.3 80.1 - - - +
125A GLU* 1.3 62.7 + - - +
126A ILE* 4.0 15.0 - - + -
139A GLU* 3.9 3.1 - - - +
140A PHE* 3.6 33.4 + - + -
152A LYS* 3.9 32.3 - - + -
173A ALA* 4.0 25.4 - - + -
174A LYS 3.3 14.8 - - - +
175A LEU* 4.2 9.2 - - + -
176A HIS* 5.2 0.2 - - - -
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Residues in contact with GLU 125 (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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123A ARG 4.0 0.2 + - - -
124A LEU* 1.3 75.9 - - - +
126A ILE* 1.3 62.6 + - - +
127A ASP* 4.1 0.6 + - - +
137A SER* 3.7 19.2 + - - +
138A GLN 3.4 5.4 - - - +
139A GLU* 3.6 33.5 - - + +
172A ARG 3.6 2.4 - - - +
173A ALA* 3.6 1.7 - - - -
174A LYS* 2.8 69.6 + - - +
176A HIS* 3.5 24.1 + - + +
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Residues in contact with ILE 126 (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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113A CYS* 4.4 3.1 - - - +
115A VAL* 3.7 26.5 - - + -
124A LEU* 4.0 11.9 - - + -
125A GLU* 1.3 76.8 - - - +
127A ASP* 1.3 62.2 + - - +
137A SER* 3.2 4.0 - - - -
138A GLN* 2.7 42.4 + - + +
140A PHE* 3.9 29.8 - - + -
152A LYS 4.1 12.1 - - - +
153A SER* 4.1 9.6 - - - -
154A LEU* 3.2 27.6 - - + +
171A CYS* 3.9 24.0 - - - -
172A ARG 3.6 4.7 - - - +
173A ALA* 5.0 1.1 - - + -
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Residues in contact with ASP 127 (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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125A GLU* 4.3 1.0 - - - +
126A ILE* 1.3 73.7 - - - +
128A LEU* 1.3 60.6 + - - +
129A LEU* 4.0 11.0 - - + -
134A LEU* 3.7 20.4 - - + +
136A LYS 3.7 3.1 - - - -
137A SER* 2.8 25.8 + - - -
154A LEU* 4.4 1.6 - - - -
170A VAL 3.6 0.9 - - - +
171A CYS* 3.4 6.1 - - - -
172A ARG* 2.5 71.7 + - + +
174A LYS* 3.0 24.4 + - - -
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Residues in contact with LEU 128 (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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97A ILE* 5.2 2.2 - - + -
111A VAL* 4.0 22.4 - - + -
113A CYS* 4.3 9.9 - - + -
127A ASP* 1.3 71.9 - - - +
129A LEU* 1.3 54.8 + - - +
134A LEU* 3.5 3.6 - - - +
135A MET* 2.8 61.6 + - + -
136A LYS 2.8 18.9 + - - +
154A LEU* 4.0 18.1 - - + +
156A VAL* 3.3 19.3 - - + -
169A LEU* 4.4 13.2 - - + -
170A VAL 3.5 4.9 - - - +
171A CYS* 3.8 31.2 - - + +
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Residues in contact with LEU 129 (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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127A ASP* 4.0 12.6 - - + +
128A LEU* 1.3 78.5 - - - +
130A LYS* 1.3 60.6 + - - +
131A GLY 4.1 7.6 - - - +
132A ASP* 4.2 14.4 - - - +
133A HIS 3.2 20.6 - - - +
134A LEU* 4.0 12.6 - - + +
135A MET* 4.3 2.0 - - - +
169A LEU* 3.2 11.3 - - - +
170A VAL* 2.9 60.3 + - + +
172A ARG* 3.9 37.0 - - + +
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Residues in contact with LYS 130 (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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129A LEU* 1.3 71.9 - - - +
131A GLY* 1.3 66.3 + - - +
132A ASP 3.3 0.3 + - - -
133A HIS* 2.9 27.1 + - + +
135A MET* 4.0 22.6 - - + +
158A PHE* 3.5 43.7 - - + -
164A ASP* 2.9 33.1 + - - +
167A LYS* 4.5 14.6 + - + +
168A VAL 3.7 3.6 - - - -
169A LEU* 4.3 4.9 - - + -
193A LEU* 4.1 18.6 - - + -
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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