Contacts of the helix formed by residues 97 - 105 (chain A) in PDB entry 2WAL
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 ASP 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL* 3.6 4.6 - - - +
96A GLY* 1.3 78.4 - - - +
98A VAL* 1.3 61.6 + - - +
99A GLN* 3.2 15.9 + - - +
100A ARG* 2.8 28.7 + - - +
101A LEU* 3.4 4.0 + - - +
157A LEU* 3.6 20.6 - - + +
159A GLU* 5.2 0.5 - - - +
1160A MLA 2.5 39.1 + - - +
149B ASN* 4.0 12.8 - - - +
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Residues in contact with VAL 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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63A ALA* 3.5 40.6 - - + +
65A GLY* 3.7 9.5 - - - +
68A ASP* 3.5 21.5 - - - +
96A GLY 4.0 0.4 + - - -
97A ASP* 1.3 69.6 + - - +
99A GLN* 1.3 76.8 + - - +
101A LEU* 3.1 5.6 + - - +
102A ALA* 3.0 18.2 + - - +
116A ASP* 3.3 38.8 - - + +
117A LEU* 3.5 19.0 - - - +
118A HIS* 3.7 3.8 - - + +
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Residues in contact with GLN 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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67A GLU* 5.5 4.9 + - - -
97A ASP* 3.6 10.6 - - - +
98A VAL* 1.3 86.6 + - - +
100A ARG* 1.3 58.4 + - - +
102A ALA* 3.1 3.3 + - - +
103A ALA* 2.9 28.6 + - - +
114A PRO* 5.9 1.4 - - - +
115A GLY 4.0 11.2 - - - +
116A ASP* 3.1 27.2 + - - +
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Residues in contact with ARG 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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27A HIS* 3.4 35.0 + - - -
97A ASP* 2.8 32.0 + - + +
99A GLN* 1.3 73.1 - - - +
101A LEU* 1.3 63.7 + - - +
103A ALA* 3.3 12.0 + - - +
104A ILE* 3.0 40.1 + - + +
157A LEU* 3.7 22.6 - - + +
158A PRO* 5.5 3.8 - - - +
159A GLU* 3.4 32.5 + - - +
1160A MLA 3.9 10.5 - - + +
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Residues in contact with LEU 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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26A LEU* 5.5 0.7 - - + -
30A LEU* 3.2 38.4 - - + -
61A VAL* 4.5 16.8 - - + +
63A ALA* 3.6 26.5 - - + -
95A VAL* 5.0 1.8 - - + -
97A ASP 3.8 2.5 - - - +
98A VAL* 3.1 9.1 + - - +
100A ARG* 1.3 79.7 - - - +
102A ALA* 1.3 61.6 + - - +
104A ILE* 3.4 5.4 + - - +
105A VAL* 3.1 30.0 + - + +
117A LEU* 3.6 22.0 - - + +
119A CYS 5.3 1.3 - - - +
120A ILE* 4.0 21.1 - - + -
1160A MLA 3.3 21.8 + - + +
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Residues in contact with ALA 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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98A VAL 3.0 6.1 + - - +
99A GLN 3.1 6.3 + - - +
101A LEU* 1.3 73.9 - - - +
103A ALA* 1.3 65.6 + - - +
105A VAL* 3.0 26.5 + - - +
106A GLY 3.5 5.3 - - - +
107A ALA 4.5 4.5 - - - +
108A GLY* 3.7 6.5 - - - -
115A GLY* 3.4 36.6 - - - +
116A ASP 4.3 0.2 - - - +
117A LEU* 3.2 23.7 - - + +
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Residues in contact with ALA 103 (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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99A GLN 2.9 12.3 + - - +
100A ARG* 3.5 21.5 - - - +
102A ALA* 1.3 77.6 - - - +
104A ILE* 1.3 62.5 + - - +
105A VAL 3.4 5.4 - - - +
108A GLY* 3.9 12.4 - - - -
109A GLU* 3.3 33.4 - - - +
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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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27A HIS* 3.7 40.6 - - + +
30A LEU* 3.8 34.1 - - + -
31A LEU* 3.4 27.0 - - + +
34A GLN* 3.7 4.5 + - - -
100A ARG* 3.0 46.2 + - + +
101A LEU* 3.7 5.8 - - - +
103A ALA* 1.3 75.8 - - - +
105A VAL* 1.3 61.9 + - - +
1160A MLA 4.3 19.5 - - + +
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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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30A LEU* 4.4 16.8 - - + -
34A GLN* 3.0 13.1 - - - +
39A LEU* 4.2 28.9 - - + -
41A ALA* 5.6 2.0 - - + -
101A LEU* 3.1 20.6 + - + +
102A ALA* 3.0 18.9 - - - +
103A ALA 3.4 5.0 - - - +
104A ILE* 1.3 79.0 - - - +
106A GLY* 1.3 72.4 + - - +
107A ALA 3.8 0.7 + - - -
108A GLY 4.1 2.4 + - - -
117A LEU* 3.1 34.3 - - + -
120A ILE* 4.6 2.2 - - + -
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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