Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 1W1W
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLN* 3.3 5.7 - - - +
100A LYS* 3.1 64.7 + - - +
102A ASN* 1.3 81.4 - - + +
104A LEU* 1.3 62.2 + - - +
105A VAL* 3.9 22.6 + - + +
122A ASP* 5.4 6.2 + - - +
134A PHE* 5.2 4.0 - - - -
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Residues in contact with LEU 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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5A VAL* 4.7 12.8 - - + -
97A PHE* 3.5 45.8 - - + +
98A TYR 3.0 20.4 - - - +
99A GLN* 3.9 15.0 - - - +
102A ASN 3.9 1.0 + - - +
103A LYS* 1.3 72.9 - - - +
105A VAL* 1.3 61.7 + - - +
106A GLU* 3.8 1.9 + - - +
122A ASP* 3.9 5.7 - - - +
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Residues in contact with VAL 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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96A ALA 3.5 1.2 - - - +
97A PHE* 3.4 2.6 - - - -
98A TYR* 2.8 45.2 + - + +
100A LYS* 4.0 24.7 - - + -
103A LYS* 4.1 25.8 - - + +
104A LEU* 1.3 75.0 - - - +
106A GLU* 1.3 61.9 + - - +
107A LEU* 3.9 7.0 - - + -
121A ILE* 3.7 24.5 - - + -
122A ASP* 3.5 12.8 - - - +
134A PHE* 3.5 30.3 - - + -
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Residues in contact with GLU 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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95A LYS* 3.0 36.1 + - + +
96A ALA 3.3 4.9 - - - +
97A PHE* 3.4 27.0 - - + -
104A LEU 3.8 1.3 + - - +
105A VAL* 1.3 71.8 - - - +
107A LEU* 1.3 72.2 + - - +
108A MET* 3.0 19.3 - - + +
120A LYS 3.7 0.5 - - - +
121A ILE* 3.6 4.2 - - - -
122A ASP* 2.8 47.2 + - - +
123A GLY* 5.0 8.7 + - - +
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Residues in contact with LEU 107 (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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49A VAL* 4.3 1.0 - - - +
50A LEU* 4.7 10.5 - - + -
94A VAL 3.7 0.5 - - - +
95A LYS* 3.1 5.2 - - - +
96A ALA* 2.7 52.9 + - + +
98A TYR* 4.7 10.8 - - + -
105A VAL* 3.9 15.9 - - + +
106A GLU* 1.3 75.2 - - - +
108A MET* 1.3 59.3 + - - +
120A LYS 3.7 1.6 - - - -
121A ILE* 4.1 14.6 - - + -
131A TYR* 3.6 18.4 - - + +
134A PHE* 3.3 42.4 - - + -
135A LEU* 3.7 25.1 - - + -
140A ILE* 4.8 3.8 - - + -
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Residues in contact with MET 108 (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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93A TYR* 4.3 11.4 - - + -
94A VAL 3.2 10.3 - - - +
95A LYS* 3.3 27.8 - - + +
106A GLU* 3.0 27.6 - - + +
107A LEU* 1.3 75.9 - - - +
109A ARG* 1.3 69.2 + - - +
110A ILE* 4.1 24.0 - - + -
118A SER 4.6 0.2 - - - -
119A TYR* 3.6 0.5 - - - -
120A LYS* 3.0 51.0 + - + +
123A GLY* 5.6 4.5 - - - +
131A TYR* 3.1 21.7 + - - -
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Residues in contact with ARG 109 (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 PHE* 2.8 76.0 + - + -
49A VAL* 4.2 4.7 - - - -
51A GLY* 4.0 0.9 - - - -
52A VAL 2.7 39.4 + - - +
62A LEU* 4.2 9.1 - - - +
93A TYR* 3.1 4.7 - - - +
94A VAL 3.0 30.4 + - - +
108A MET* 1.3 76.6 - - - +
110A ILE* 1.3 67.8 + - - +
117A THR* 3.6 20.6 + - - +
118A SER 3.3 11.0 - - - +
119A TYR* 2.6 43.3 + - + -
128A TYR* 4.0 4.2 + - - -
131A TYR* 4.1 8.3 - - - +
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Residues in contact with ILE 110 (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 PHE* 4.4 0.9 - - - -
91A SER* 4.5 11.4 - - - +
92A ALA 3.4 11.9 - - - +
93A TYR* 3.7 15.7 - - + -
108A MET* 4.1 21.1 - - + -
109A ARG* 1.3 80.9 - - - +
111A ILE* 1.3 73.8 + - - +
112A SER* 4.9 4.9 - - - +
116A ASP 4.4 0.7 - - - +
117A THR* 3.0 9.4 - - - -
118A SER* 2.8 48.9 + - - +
120A LYS* 4.3 22.7 - - + +
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Residues in contact with ILE 111 (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 PHE* 4.7 2.0 - - + -
48A PHE* 3.1 28.9 - - + -
62A LEU* 4.1 22.0 - - + +
63A LYS* 5.1 0.7 - - - +
65A LEU* 3.3 38.8 - - + -
66A ILE* 3.4 11.5 - - + +
91A SER* 3.2 4.2 - - - -
92A ALA* 2.9 41.8 + - + +
110A ILE* 1.3 73.2 - - - +
112A SER* 1.3 70.2 + - - +
115A GLY* 4.3 10.8 - - - +
116A ASP 3.7 1.8 - - - -
117A THR* 3.9 20.0 - - + -
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Residues in contact with SER 112 (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 LYS* 5.6 2.1 - - - -
66A ILE* 3.6 4.5 - - - +
90A GLN 3.6 6.1 - - - -
91A SER* 4.1 9.1 - - - -
110A ILE* 5.0 4.9 - - - +
111A ILE* 1.3 79.7 - - - +
113A ARG* 1.3 64.6 + - - +
114A ASN* 3.0 30.1 - - - -
115A GLY* 2.9 13.9 + - - -
116A ASP* 3.2 15.2 + - - +
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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