Contacts of the strand formed by residues 98 - 105 (chain A) in PDB entry 2WA2
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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.6 33.9 - - + +
75A LYS 3.8 2.2 - - - +
76A GLY 3.7 5.8 - - - +
78A VAL* 3.8 14.6 - - + -
92A ALA 3.2 27.8 - - - +
93A ALA* 4.5 4.5 - - - -
95A GLN* 3.2 15.8 + - + +
96A PRO 4.2 4.0 - - - +
97A ASN* 1.3 78.4 - - - +
99A ARG* 1.3 62.9 + - - +
100A GLU* 3.7 22.4 - - - +
101A VAL* 3.8 12.1 - - + -
124A LEU* 4.1 13.5 - - + +
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Residues in contact with ARG 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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76A GLY* 2.8 22.3 + - - +
77A THR* 5.6 1.0 + - - +
97A ASN 3.6 8.0 + - - +
98A VAL* 1.3 76.9 - - - +
100A GLU* 1.3 70.6 + - + +
124A LEU* 3.7 22.9 - - - +
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Residues in contact with GLU 100 (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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76A GLY 3.3 3.3 + - - +
77A THR* 2.9 37.9 + - + +
78A VAL 3.0 24.6 + - - -
98A VAL* 3.7 1.9 - - - +
99A ARG* 1.3 87.6 - - + +
101A VAL* 1.3 69.3 + - - +
102A LYS* 3.6 28.2 + - + +
124A LEU* 3.5 14.8 - - - +
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Residues in contact with VAL 101 (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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78A VAL* 3.3 14.4 - - + +
80A ASP* 4.5 6.1 - - + -
89A SER* 3.6 37.0 - - - +
92A ALA* 4.1 6.3 - - + -
93A ALA* 3.9 25.1 - - + +
98A VAL* 3.8 18.2 - - + -
100A GLU* 1.3 79.1 - - - +
102A LYS* 1.3 69.8 + - - +
124A LEU* 2.9 9.3 + - + +
125A ILE* 3.3 12.7 - - + +
126A THR* 2.8 28.4 + - - +
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Residues in contact with LYS 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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77A THR* 4.4 7.1 - - + +
78A VAL 2.9 12.9 + - - +
79A VAL* 3.2 5.7 - - + -
80A ASP 2.9 28.3 + - - -
100A GLU* 3.6 34.2 + - + -
101A VAL* 1.3 75.9 - - - +
103A ALA* 1.3 53.0 + - - +
104A TYR* 3.4 29.0 - - + +
126A THR* 3.7 13.0 - - - +
139A PHE* 3.6 36.3 - - + -
140A GLN 5.1 0.8 + - - -
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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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80A ASP* 3.5 6.3 - - - -
83A CYS* 3.9 7.6 - - + -
89A SER* 3.2 26.5 - - - +
101A VAL* 4.6 0.2 - - + -
102A LYS* 1.3 71.8 - - - +
104A TYR* 1.3 63.6 + - - +
125A ILE* 4.1 4.9 - - + -
126A THR 2.9 10.4 + - - +
127A PHE* 3.5 27.1 - - + -
128A LYS* 2.8 30.7 + - - +
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.6 1.6 - - + -
80A ASP 2.9 7.9 + - - +
81A LEU* 4.1 16.2 - - + -
82A GLY 2.8 27.6 + - - -
83A CYS* 2.8 7.5 + - - -
102A LYS* 3.4 40.9 - - + +
103A ALA* 1.3 79.2 - - - +
105A THR* 1.3 61.6 + - - +
126A THR* 5.7 1.3 - - + -
128A LYS* 3.3 42.1 - - + +
131A VAL* 4.4 10.8 - - + -
133A VAL* 3.7 21.1 - - + -
136A MET* 4.0 19.3 - - + -
139A PHE* 3.5 34.4 - + - -
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Residues in contact with THR 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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83A CYS* 3.6 13.7 + - - -
84A GLY* 3.0 26.5 + - - +
104A TYR* 1.3 77.1 - - - +
106A LEU* 1.3 66.7 + - - +
107A GLY 4.1 2.9 - - - +
112A GLU 3.8 19.1 + - - +
114A PRO* 3.9 18.6 - - + -
128A LYS 3.1 6.7 + - - -
129A SER* 3.2 10.7 - - - +
130A LYS 3.1 17.8 + - - -
131A VAL* 3.3 11.8 + - - +
1248A SAM 3.5 26.0 + - - -
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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