Contacts of the helix formed by residues 122 - 131 (chain A) in PDB entry 2VLA
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASP 3.7 0.8 + - - -
121A LYS* 1.3 77.2 - - - +
123A ASP* 1.3 63.2 + - - +
125A VAL* 3.2 9.7 + - + +
126A ILE* 2.9 38.2 + - + +
260A PHE* 3.8 32.3 - - + +
266A LYS* 3.8 30.7 - - + +
270A PHE* 4.2 23.6 - - + -
211M C 3.6 22.4 + - - +
212M C 3.5 27.5 + - - +
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Residues in contact with ASP 123 (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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121A LYS* 3.2 28.9 - - - +
122A LEU* 1.3 74.8 - - - +
124A LYS* 1.3 73.8 + - - +
126A ILE* 3.5 10.9 + - - +
127A GLU* 3.0 39.5 + - - +
210M A 3.8 22.8 - - - +
211M C 3.6 29.4 + - - +
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Residues in contact with LYS 124 (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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10A ARG* 5.7 1.3 - - - +
12A THR* 5.9 5.4 - - - +
120A ASP* 4.0 10.8 - - + -
121A LYS* 2.9 9.7 + - + +
123A ASP* 1.3 92.3 + - - +
125A VAL* 1.3 64.7 + - - +
127A GLU* 3.3 28.7 + - - +
128A LYS* 3.0 34.3 + - - +
106L C 3.5 49.3 + - - +
107L C 3.4 20.5 + - - -
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Residues in contact with VAL 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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116A PRO* 5.1 4.5 - - + -
117A ASN 3.6 21.3 - - - +
120A ASP* 3.6 20.8 - - + +
121A LYS 3.0 19.0 + - - +
122A LEU* 3.2 12.3 + - + +
124A LYS* 1.3 75.9 - - - +
126A ILE* 1.3 57.9 + - - +
128A LYS* 3.1 6.4 + - - +
129A VAL* 2.9 33.2 + - + +
260A PHE* 3.8 25.6 - - + -
269A PHE* 3.7 31.0 - - + -
270A PHE* 4.5 1.6 - - + -
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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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122A LEU* 2.9 39.9 + - + +
123A ASP* 3.7 9.2 - - - +
125A VAL* 1.3 74.4 - - - +
127A GLU* 1.3 59.0 + - + +
129A VAL* 3.9 5.7 - - - +
130A GLY* 2.8 27.2 + - - -
260A PHE* 4.0 36.3 - - + +
261A THR* 6.5 0.4 - - + -
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Residues in contact with GLU 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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9A PHE* 4.3 14.5 - - + -
123A ASP* 3.0 25.7 + - - +
124A LYS* 3.5 35.5 + - - +
125A VAL 3.2 0.2 - - - -
126A ILE* 1.3 77.8 - - + +
128A LYS* 1.3 57.2 + - + +
130A GLY* 3.2 2.1 + - - -
131A ALA* 3.0 28.6 + - - +
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Residues in contact with LYS 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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9A PHE* 4.2 17.0 - - + -
10A ARG 5.1 1.3 - - - -
11A CYS* 3.6 26.4 - - - +
12A THR* 3.0 38.4 + - - +
115A PHE* 4.2 8.9 - - + -
116A PRO* 4.4 21.5 - - + -
120A ASP* 2.6 32.7 + - - +
124A LYS* 3.0 25.2 + - - +
125A VAL* 3.7 4.0 - - - +
127A GLU* 1.3 73.9 - - + +
129A VAL* 1.3 66.4 + - - +
131A ALA 3.2 6.6 + - - -
133A ILE* 3.2 37.5 + - + +
256A TYR* 4.4 0.4 - - - -
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Residues in contact with VAL 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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116A PRO* 4.0 18.8 - - + -
125A VAL* 2.9 22.0 + - + +
126A ILE* 3.9 5.6 - - - +
128A LYS* 1.3 77.4 - - - +
130A GLY* 1.3 62.6 + - - +
132A LYS* 3.0 14.0 + - - +
255A ALA* 4.2 12.3 - - + +
256A TYR* 3.5 36.3 - - + -
260A PHE* 3.9 31.0 - - + -
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Residues in contact with GLY 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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126A ILE* 2.8 18.7 + - - -
127A GLU* 3.2 2.9 + - - -
129A VAL* 1.3 78.1 - - - +
131A ALA* 1.3 58.4 + - - +
132A LYS* 3.3 7.7 + - - +
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Residues in contact with ALA 131 (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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9A PHE* 3.7 27.4 - - + -
127A GLU 3.0 15.5 + - - +
128A LYS 3.7 4.7 - - - +
129A VAL 3.1 0.4 - - - -
130A GLY* 1.3 75.5 - - - +
132A LYS* 1.3 63.6 + - - +
133A ILE* 3.3 7.4 + - + -
168A LEU* 4.2 8.1 - - + -
172A GLN* 2.8 32.4 + - - +
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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