Contacts of the helix formed by residues 126 - 135 (chain L) in PDB entry 1VQ9
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 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6970 G 3.5 32.8 - - - -
6980 A 3.2 24.3 + - - -
107L LYS* 4.6 0.4 - - - +
108L VAL 3.2 9.5 + - - -
109L LEU* 4.4 6.1 - - - -
110L GLY 3.3 1.6 + - - -
125L PHE* 1.3 78.8 - - - +
127L GLU* 1.3 69.2 + - - +
128L GLY 4.4 0.7 - - - -
129L ALA* 2.7 35.0 + - - +
130L ARG* 3.0 7.3 + - - +
149L ARG* 5.2 0.2 - - - +
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Residues in contact with GLU 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6970 G 3.0 18.2 + - - +
125L PHE 4.2 0.2 + - - -
126L SER* 1.3 72.9 - - - +
128L GLY* 1.3 63.2 + - - +
130L ARG* 3.1 18.5 + - - +
131L GLU* 3.1 36.5 + - + +
149L ARG* 5.9 1.4 - - - +
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Residues in contact with GLY 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6970 G 5.4 1.0 + - - -
6980 A 4.0 13.4 + - - -
110L GLY* 4.2 5.6 - - - -
126L SER* 3.2 2.6 + - - -
127L GLU* 1.3 79.5 + - - +
129L ALA* 1.3 64.3 + - - +
131L GLU* 4.0 10.3 - - - -
132L LYS* 3.0 35.9 + - - +
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L VAL* 4.4 3.2 - - - +
108L VAL* 3.4 32.5 - - + +
110L GLY* 3.7 15.9 - - - +
125L PHE* 4.0 5.2 - - + -
126L SER* 2.7 39.3 + - - +
128L GLY* 1.3 73.2 - - - +
130L ARG* 1.3 57.2 + - - +
132L LYS* 4.1 1.9 - - - +
133L VAL* 3.0 31.0 + - - +
140L VAL* 5.5 0.9 - - - -
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Residues in contact with ARG 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L PHE* 4.1 30.3 + - + +
126L SER 3.0 10.6 + - - +
127L GLU* 3.4 9.4 - - - +
129L ALA* 1.3 71.5 - - - +
131L GLU* 1.3 59.2 + - + +
132L LYS 3.0 1.8 - - - -
133L VAL* 2.5 31.6 + - - -
134L GLU* 2.9 34.1 + - - +
140L VAL* 3.9 38.5 - - + +
142L LEU* 4.5 21.8 - - - +
149L ARG* 4.5 11.9 - - - +
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L GLU* 3.1 44.5 + - + +
128L GLY* 4.1 7.9 - - - +
130L ARG* 1.3 78.6 - - + +
132L LYS* 1.3 57.7 - - + +
134L GLU* 4.4 8.9 + - - +
135L GLY* 3.0 26.0 + - - -
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Residues in contact with LYS 132 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6980 A 4.6 1.7 + - - -
6990 C 3.0 21.6 + - - -
7000 A 5.6 0.2 + - - -
66L VAL* 4.7 4.7 - - + -
110L GLY* 2.8 31.8 + - - +
112L GLY 2.8 27.3 + - - +
113L GLN* 5.2 1.1 - - - -
114L VAL* 4.0 21.2 - - + +
128L GLY* 3.0 21.4 + - - +
129L ALA* 4.1 2.9 - - - +
130L ARG 2.7 4.8 + - - -
131L GLU* 1.3 74.3 - - + +
133L VAL* 1.3 66.2 + - - +
135L GLY* 3.4 8.8 + - - -
136L ALA* 3.4 12.6 + - - +
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Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L VAL* 4.4 11.2 - - + -
114L VAL* 4.7 12.1 - - + -
116L HIS 5.1 0.9 - - - +
118L LEU* 3.5 31.6 - - + +
120L LEU* 3.7 26.2 - - + -
129L ALA* 3.0 17.7 - - + +
130L ARG 2.5 12.1 + - - +
132L LYS* 1.3 68.4 - - - +
134L GLU* 1.3 65.5 + - - +
136L ALA* 3.0 15.1 + - - +
138L GLY* 3.1 13.4 + - - -
139L SER 3.5 21.3 - - - +
140L VAL* 4.3 9.6 - - + -
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Residues in contact with GLU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L ARG* 2.9 35.9 + - + +
131L GLU* 4.4 9.5 + - - +
133L VAL* 1.3 68.6 - - + +
135L GLY* 1.3 53.9 + - - +
136L ALA 2.6 5.5 + - - -
137L GLY* 2.6 30.5 + - - -
138L GLY 3.2 20.4 + - - +
139L SER* 5.0 5.5 - - - -
140L VAL* 5.5 5.6 + - + +
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Residues in contact with GLY 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L GLU 3.0 20.6 + - - -
132L LYS* 3.7 4.5 - - - -
133L VAL 3.2 0.4 - - - -
134L GLU* 1.3 74.6 - - - +
136L ALA* 1.3 57.0 + - - +
137L GLY 3.4 1.5 + - - -
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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