Contacts of the strand formed by residues 126 - 133 (chain A) in PDB entry 1NWW
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 LYS 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 2.8 25.8 + - - +
46A TYR* 3.5 16.4 - - - +
47A PHE 4.5 4.7 - - - +
48A ALA* 3.7 22.9 - - + +
122A LEU* 3.2 5.0 - - - -
123A THR 2.9 31.6 + - - +
124A GLU* 4.1 8.3 - - + +
125A GLY* 1.3 85.9 + - - +
127A ILE* 1.3 64.8 + - - +
128A THR* 3.4 2.1 + - - +
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Residues in contact with ILE 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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27A ILE* 5.5 3.6 - - + -
28A VAL* 5.9 2.5 - - + -
31A PHE* 4.0 34.1 - - + -
46A TYR* 2.9 39.2 + - + +
47A PHE* 3.6 26.0 - - + -
48A ALA 3.0 17.5 + - - -
51A THR* 2.8 19.2 + - - -
120A PHE* 4.5 9.6 - - + -
121A GLN 3.4 5.4 - - - +
122A LEU* 4.4 17.7 - - + -
126A LYS* 1.3 70.5 - - - +
128A THR* 1.3 53.4 + - - +
129A GLY 3.5 29.8 - - - +
130A TRP* 4.1 4.0 - - + -
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Residues in contact with THR 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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48A ALA* 4.2 9.2 - - + -
50A ASP 3.8 16.8 - - - +
51A THR* 3.2 24.4 - - - -
52A MET* 3.2 3.1 + - - +
121A GLN* 2.8 29.9 + - - +
123A THR* 3.4 36.7 + - - +
126A LYS 3.9 4.3 - - - +
127A ILE* 1.3 72.9 - - - +
129A GLY* 1.3 57.2 + - - +
901A MES 3.3 19.5 + - - +
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Residues in contact with GLY 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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52A MET* 3.3 16.6 - - - -
119A VAL 4.4 0.2 - - - -
120A PHE* 3.3 4.4 - - - -
121A GLN* 2.9 44.3 + - - +
127A ILE* 3.5 8.9 - - - +
128A THR* 1.3 83.1 + - - +
130A TRP* 1.3 61.2 + - - -
131A ARG* 4.4 2.5 - - - -
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Residues in contact with TRP 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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31A PHE* 3.6 32.3 - + - -
32A MET* 4.7 0.2 - - + -
35A LEU* 4.0 20.2 - - + -
47A PHE* 3.7 16.6 - + + -
52A MET* 3.0 10.8 + - - +
53A TYR* 3.2 47.6 - + + -
54A GLN 2.9 24.9 + - - -
71A LEU* 4.3 12.6 - - + -
80A ILE* 6.2 0.4 - - + -
99A ARG* 4.3 7.6 - - - +
119A VAL 3.3 6.5 - - - -
120A PHE* 3.2 36.9 - + + -
127A ILE* 4.1 12.1 - - + -
129A GLY* 1.3 74.6 - - - +
131A ARG* 1.3 67.0 + - - +
132A ASP* 3.0 39.2 + - - -
900A HPN 4.3 5.6 - - - -
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Residues in contact with ARG 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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52A MET* 3.6 19.5 - - + -
54A GLN* 3.2 4.9 - - + -
56A MET* 3.8 24.0 - - - -
118A GLY* 3.2 2.4 - - - -
119A VAL* 2.9 54.5 + - + +
121A GLN* 2.7 40.4 + - - +
129A GLY* 4.2 5.3 - - - -
130A TRP* 1.3 77.5 - - - +
132A ASP* 1.3 61.9 + - - +
133A TYR* 3.9 6.2 - - + -
10B TRP* 3.3 55.9 - - - +
87B HIS* 3.8 2.2 + - - -
98B GLU* 2.8 39.5 + - - -
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Residues in contact with ASP 132 (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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53A TYR* 5.5 0.6 - - + -
54A GLN 3.0 6.6 + - - +
55A ASN* 3.7 18.5 - - - +
56A MET* 2.9 30.1 + - - +
99A ARG* 2.8 43.9 + - - -
116A ILE* 3.6 9.9 - - + -
117A LEU 3.9 1.1 - - - -
118A GLY* 3.3 10.7 - - - -
130A TRP* 3.0 33.9 + - + -
131A ARG* 1.3 71.2 - - - +
133A TYR* 1.3 61.8 - - - +
134A PHE* 3.8 8.7 - - + -
900A HPN 3.3 8.1 + - - -
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Residues in contact with TYR 133 (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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56A MET* 3.6 41.6 - - + +
116A ILE* 3.5 2.6 - - - -
117A LEU 2.8 35.0 + - - +
119A VAL* 4.4 0.4 - - + -
131A ARG* 3.9 11.7 - - + -
132A ASP* 1.3 73.9 - - - +
134A PHE* 1.3 66.3 + - - +
10B TRP* 4.1 4.3 - - - -
98B GLU* 2.6 38.2 + - + +
99B ARG 5.0 1.4 + - - -
115B SER* 3.7 16.3 - - - -
116B ILE 3.5 24.1 + - - -
117B LEU* 3.4 41.3 - - + -
133B TYR* 3.7 27.5 - - + +
134B PHE* 4.6 2.0 - - - +
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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