Contacts of the helix formed by residues 114 - 119 (chain A) in PDB entry 1NQG
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 ARG 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A THR 4.4 4.9 - - - -
12A ALA* 3.5 28.2 + - - +
22A VAL* 4.9 2.2 - - - +
24A ALA* 3.7 23.2 - - - +
110A ILE* 3.5 34.8 - - - +
111A ARG 4.3 6.3 + - - -
112A GLY* 3.6 3.7 + - - +
113A PRO* 1.3 86.2 + - - +
115A SER* 1.3 61.2 + - - +
116A ALA 3.1 2.9 - - - -
117A VAL* 3.3 18.4 + - + +
118A TYR* 2.9 38.8 + - + +
122A ALA* 3.2 13.7 + - - +
126A VAL* 4.0 15.7 - - + -
354A GLU* 4.0 23.2 + - - +
372A GLN* 3.0 25.6 + - - +
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Residues in contact with SER 115 (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 PRO 3.8 0.8 - - - -
114A ARG* 1.3 73.6 - - - +
116A ALA* 1.3 56.9 + - - +
117A VAL 2.8 6.0 + - - -
118A TYR 3.0 2.9 + - - -
119A GLY* 2.4 55.1 + - - +
122A ALA* 3.7 8.6 + - - -
358A ARG* 3.0 9.9 - - - -
360A ASP* 4.6 0.2 - - - +
370A THR* 3.4 14.1 - - - +
372A GLN* 3.9 1.2 - - - +
391A THR 4.6 1.0 + - - -
392A SER* 3.2 31.6 - - - -
393A TYR* 3.4 14.9 + - - -
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Residues in contact with ALA 116 (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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114A ARG 3.1 0.2 - - - -
115A SER* 1.3 76.1 - - - +
117A VAL* 1.3 63.7 - - - +
341A TYR* 3.6 4.5 - - - +
356A ALA* 3.5 29.1 - - + +
357A ALA 3.5 9.9 - - - +
358A ARG* 3.5 15.5 - - - +
370A THR* 3.0 30.2 - - + +
371A TRP* 3.8 7.4 - - - +
372A GLN* 3.9 16.8 - - + +
391A THR 4.8 0.6 + - - +
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Residues in contact with VAL 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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12A ALA 4.2 16.8 - - - +
13A ASN* 5.0 1.8 - - - -
14A ARG* 2.8 36.7 + - + +
114A ARG* 3.3 16.4 + - + +
115A SER 3.5 1.1 - - - -
116A ALA* 1.3 88.4 - - + +
118A TYR* 1.3 90.0 + - + +
341A TYR* 3.9 11.3 - - + -
343A THR* 4.1 13.9 - - + -
356A ALA* 3.6 19.3 - - + -
358A ARG* 2.8 12.6 + - - +
372A GLN* 5.4 0.9 - - - +
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Residues in contact with TYR 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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10A VAL* 5.4 0.3 - - - +
11A THR* 2.7 41.8 + - + +
14A ARG* 3.5 44.4 + - + +
77A LEU* 3.6 19.1 - - + +
79A LEU* 3.5 29.7 - - + +
82A GLY* 4.6 3.9 - - - -
84A ARG* 3.5 18.0 + - - -
114A ARG* 2.9 30.3 + - + +
117A VAL* 1.3 100.9 - - + +
119A GLY* 1.3 58.8 + - - +
126A VAL* 4.2 13.5 - - + -
128A ASN* 5.1 1.0 + - - -
299A GLN* 5.9 0.2 - - - -
316A ASP* 4.4 4.0 - - - +
358A ARG* 3.3 13.4 + - - +
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Residues in contact with GLY 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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84A ARG* 4.1 1.1 - - - -
115A SER* 2.4 52.9 + - - -
118A TYR* 1.3 72.4 - - - +
120A SER* 1.3 65.8 + - - +
121A ASP 3.5 0.2 + - - -
122A ALA* 3.7 4.0 + - - +
358A ARG* 3.3 20.6 - - - +
360A ASP* 3.9 7.9 - - - -
393A TYR* 3.7 4.5 - - - -
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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