Contacts of the strand formed by residues 125 - 130 (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 GLY 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.2 6.1 - - - +
75A HIS 4.4 1.2 + - - -
76A VAL* 3.5 8.9 - - - +
77A LEU 3.4 19.8 + - - -
109A TYR* 5.2 2.0 - - - -
110A ILE 3.5 3.1 - - - -
111A ARG* 3.9 2.9 - - - -
112A GLY 2.9 24.5 - - - -
122A ALA* 4.2 5.2 - - - -
123A ILE 3.4 1.7 - - - -
124A GLY* 1.3 77.6 - - - +
126A VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.8 26.2 - - + -
77A LEU* 3.4 26.9 - - + +
79A LEU* 4.2 12.8 - - + -
109A TYR* 3.2 22.1 - - - -
110A ILE* 2.8 23.2 + - + +
114A ARG* 4.0 27.6 - - + -
118A TYR* 4.2 7.0 - - + -
122A ALA* 4.0 4.9 - - + -
125A GLY* 1.3 76.0 - - - +
127A VAL* 1.3 80.7 + - - +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.1 32.8 - - + -
52A VAL* 6.4 0.9 - - + -
66A ILE* 5.9 3.4 - - + -
68A ILE* 5.4 3.6 - - + -
76A VAL* 4.2 15.5 - - + -
77A LEU 2.6 11.1 + - - +
78A VAL* 3.5 16.2 - - + +
79A LEU 2.7 28.6 + - - +
107A VAL* 4.4 7.9 - - + -
108A GLU 3.9 1.6 - - - -
109A TYR* 3.8 21.3 - - + -
126A VAL* 1.3 85.4 - - - +
128A ASN* 1.3 63.0 + - - +
129A ILE* 4.4 14.8 - - + -
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Residues in contact with ASN 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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10A VAL* 4.9 4.9 - - - +
11A THR* 3.0 45.5 + - + +
79A LEU* 3.3 12.8 - - + +
81A ASP 3.6 3.6 + - - -
82A GLY* 3.3 31.3 + - - +
107A VAL* 3.3 3.3 - - - -
108A GLU 2.8 39.3 + - - +
118A TYR* 5.1 0.8 + - - -
126A VAL* 4.1 2.2 - - + +
127A VAL* 1.3 76.5 - - - +
129A ILE* 1.3 65.2 + - - +
130A ILE* 3.5 18.6 + - - +
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Residues in contact with ILE 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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42A VAL* 4.3 14.6 - - + -
46A LEU* 5.9 0.7 - - + -
78A VAL* 4.5 2.5 - - + -
79A LEU 2.7 13.1 + - - +
80A ILE* 3.4 23.0 - - + +
81A ASP 2.9 21.1 + - - -
96A LEU* 3.7 40.6 - - + -
99A PHE* 4.4 13.2 - - + -
104A VAL* 3.9 25.4 - - + -
106A ARG 3.8 5.2 - - - +
107A VAL* 4.6 10.3 - - + +
127A VAL* 4.4 11.7 - - + -
128A ASN* 1.3 72.2 - - - +
130A ILE* 1.3 64.2 + - - +
131A THR* 4.7 4.3 - - + -
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Residues in contact with ILE 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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10A VAL* 5.6 4.0 - - + -
81A ASP* 3.2 12.6 - - - +
103A LEU 4.1 0.2 - - - +
104A VAL* 4.3 0.9 - - - -
105A GLN* 3.0 25.5 + - - +
106A ARG* 2.8 35.2 + - + +
108A GLU* 3.7 39.5 - - + +
128A ASN* 3.9 24.9 - - - +
129A ILE* 1.3 75.6 - - - +
131A THR* 1.3 61.1 + - - +
132A THR* 3.3 22.9 - - - +
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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