Contacts of the strand formed by residues 96 - 106 (chain A) in PDB entry 1NW6
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASP* 3.2 6.2 - - - +
59A VAL* 3.3 14.4 - - + +
60A GLN 4.0 10.5 - - - +
62A ILE* 3.7 24.0 - - + -
92A ALA 3.2 19.3 + - - +
93A GLU* 3.3 8.4 + - - +
95A VAL* 1.3 77.3 - - - +
97A SER* 1.3 65.8 + - - +
100A GLY* 4.3 2.2 - - - -
101A SER* 3.3 36.6 - - - +
102A ILE* 4.0 9.2 - - + +
132A MET* 3.4 32.1 - - + -
164A LYS* 2.8 33.0 + - + -
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Residues in contact with SER 97 (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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57A ASP* 3.6 20.0 - - - +
58A SER 5.3 0.7 - - - -
59A VAL 2.8 17.9 + - - -
60A GLN* 3.5 9.0 + - - -
95A VAL 3.7 1.0 + - - -
96A LEU* 1.3 77.4 - - - +
98A PRO* 1.3 69.0 - - - +
99A THR* 3.3 19.8 + - - -
100A GLY* 2.8 25.9 + - - +
164A LYS* 3.5 9.6 - - - +
314A ARG* 6.1 2.7 - - - -
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Residues in contact with PRO 98 (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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57A ASP* 4.1 19.5 - - + +
97A SER* 1.3 87.9 - - - +
99A THR* 1.3 64.2 + - + +
100A GLY 3.3 0.2 - - - -
164A LYS* 4.5 4.7 - - + -
165A THR* 2.7 44.6 + - + +
167A LYS* 4.0 21.3 - - - +
168A TYR 4.5 0.2 + - - -
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Residues in contact with THR 99 (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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60A GLN* 3.0 24.6 + - - -
97A SER* 3.3 6.1 + - - -
98A PRO* 1.3 83.2 - - + +
100A GLY* 1.3 61.0 + - - +
101A SER* 4.6 0.2 + - - -
167A LYS* 3.4 29.6 - - + +
168A TYR* 3.5 4.2 - - - +
169A PHE* 3.0 27.9 + - - +
241A HIS* 5.0 4.2 + - - -
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.0 21.5 - - - -
96A LEU* 4.3 7.0 - - - -
97A SER* 2.8 22.7 + - - -
98A PRO 3.3 0.2 - - - -
99A THR* 1.3 80.0 - - - +
101A SER* 1.3 63.7 + - - -
163A ALA* 3.7 1.6 - - - +
164A LYS* 2.9 26.5 + - - +
165A THR 4.7 0.2 + - - -
168A TYR* 4.5 0.7 - - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.0 6.9 + - - +
61A LEU* 3.3 15.3 - - - -
62A ILE 3.1 21.1 + - - -
96A LEU* 3.3 13.4 - - - +
99A THR 4.6 0.7 + - - -
100A GLY* 1.3 75.0 + - - -
102A ILE* 1.3 60.7 + - - +
161A TRP* 2.9 34.7 + - - -
162A PHE 3.2 6.3 - - - -
163A ALA* 3.8 8.3 - - - +
168A TYR* 4.0 7.4 - - - +
169A PHE 4.8 3.6 + - - -
239A LEU* 4.5 10.8 + - - +
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Residues in contact with ILE 102 (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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61A LEU* 4.9 0.4 - - - -
62A ILE* 3.4 32.1 - - + +
64A CYS* 3.9 18.4 - - + -
88A TRP* 5.2 0.2 - - + -
89A LEU* 5.1 5.4 - - + -
92A ALA* 4.0 22.2 - - + -
96A LEU* 4.0 8.1 - - + -
101A SER* 1.3 75.2 - - - +
103A ALA* 1.3 61.8 + - - +
104A ILE* 3.9 24.7 - - + -
126A MET* 5.6 1.3 - - + -
132A MET* 4.0 15.3 - - + -
160A ALA 3.4 2.6 - - - +
161A TRP* 3.6 3.9 - - - -
162A PHE* 2.8 56.1 + - + +
249A PHE* 5.0 1.1 - - + -
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Residues in contact with ALA 103 (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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61A LEU* 4.5 1.7 - - + +
62A ILE 3.0 11.8 + - - +
63A ILE* 4.0 4.9 - - + -
64A CYS* 2.9 29.1 + - - +
102A ILE* 1.3 73.6 - - - +
104A ILE* 1.3 60.5 + - - +
105A PHE* 4.0 3.1 + - + -
159A ILE* 4.0 7.6 - - + -
160A ALA 3.5 4.9 - - - -
161A TRP* 4.4 2.5 - - - +
235A LEU* 3.8 40.6 - - + -
239A LEU* 4.7 7.6 - - + -
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Residues in contact with ILE 104 (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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64A CYS* 3.2 14.1 - - + +
66A PRO* 4.3 5.6 - - + -
68A TYR* 3.8 6.1 - - - +
89A LEU* 3.9 27.1 - - + -
102A ILE* 3.9 24.7 - - + -
103A ALA* 1.3 75.7 - - - +
105A PHE* 1.3 70.5 + - - +
119A LEU* 3.7 23.8 - - + +
122A ILE* 4.1 20.4 - - + -
126A MET* 5.4 1.3 - - + -
159A ILE* 3.4 2.5 - - - +
160A ALA* 2.8 41.6 + - + +
162A PHE* 4.0 24.0 - - + -
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Residues in contact with PHE 105 (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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63A ILE* 4.2 9.6 - - + -
64A CYS 2.7 21.1 + - - +
65A ASP* 3.5 28.7 - - + +
66A PRO* 3.7 7.3 - - - +
68A TYR* 2.6 29.3 + - - -
103A ALA 4.3 4.3 - - - -
104A ILE* 1.3 73.9 - - - +
106A GLY* 1.3 53.2 + - - +
119A LEU* 4.5 0.2 - - - -
140A TRP* 4.1 12.1 - + - -
157A GLU* 3.5 20.4 - - - +
158A GLU 3.4 4.9 - - - -
159A ILE* 3.7 25.4 - - + +
227A LYS* 4.0 15.9 - - + -
231A VAL* 3.9 18.4 - - + -
232A ILE* 3.7 28.9 - - + -
235A LEU* 3.9 22.2 - - + -
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Residues in contact with GLY 106 (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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68A TYR* 3.4 20.4 - - - -
104A ILE 3.8 0.8 + - - -
105A PHE* 1.3 76.6 - - - +
107A GLY* 1.3 62.1 + - - -
119A LEU* 3.9 9.6 - - - +
157A GLU* 3.7 9.6 + - - +
158A GLU* 2.8 37.7 + - - +
401A SFG 5.7 0.4 - - - -
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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