Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 2W7W
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 THR 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 3.8 7.2 + - + +
89A PRO* 1.3 79.6 - - - +
91A GLY* 1.3 68.9 + - - +
93A VAL* 4.1 1.6 - - - +
94A ALA* 3.4 13.7 + - - -
185A TRP* 5.3 2.7 - - - +
189A GLU* 3.4 14.4 - - - +
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Residues in contact with GLY 91 (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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90A THR* 1.3 77.4 - - - +
92A ALA* 1.3 65.1 + - - -
93A VAL 3.3 0.5 + - - -
94A ALA* 3.7 2.9 - - - +
95A ALA* 3.4 20.1 + - - +
189A GLU* 3.9 5.6 - - - -
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Residues in contact with ALA 92 (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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91A GLY* 1.3 72.9 - - - -
93A VAL* 1.3 57.5 + - - +
95A ALA* 3.6 5.8 + - - +
96A ALA* 3.1 27.4 + - - +
189A GLU* 2.9 18.8 + - + +
192A LEU* 3.5 17.9 - - + +
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Residues in contact with VAL 93 (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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89A PRO* 4.0 4.0 - - + -
90A THR 4.1 2.7 - - - +
92A ALA* 1.3 74.9 - - - +
94A ALA* 1.3 66.3 + - - +
96A ALA* 3.2 4.1 + - + +
97A ILE* 2.9 43.4 + - + +
126A LEU* 5.7 1.1 - - + -
185A TRP* 3.9 25.8 - - + +
188A VAL* 3.9 12.8 - - + +
189A GLU* 3.0 50.9 + - - +
192A LEU* 3.7 17.5 - - + -
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Residues in contact with ALA 94 (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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89A PRO* 3.4 37.6 - - + +
90A THR* 3.4 18.9 + - - -
91A GLY 3.4 3.1 + - - +
93A VAL* 1.3 77.4 - - - +
95A ALA* 1.3 56.7 + - - +
97A ILE* 3.3 3.3 + - - +
98A ASP* 3.0 37.4 + - - +
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Residues in contact with ALA 95 (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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91A GLY 3.4 9.7 + - - +
92A ALA* 4.0 7.6 - - - +
93A VAL 3.2 0.8 - - - -
94A ALA* 1.3 75.6 - - - +
96A ALA* 1.3 60.1 + - - +
98A ASP* 3.9 7.0 - - - +
99A ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 96 (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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92A ALA 3.1 19.1 + - - +
93A VAL* 3.4 8.5 - - + +
95A ALA* 1.3 76.9 - - - +
97A ILE* 1.3 57.8 + - - +
99A ALA* 3.4 6.5 + - - +
100A ALA* 3.0 30.8 + - - +
134A LEU* 3.5 21.2 - - + +
192A LEU* 4.3 16.6 - - + -
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Residues in contact with ILE 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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89A PRO* 4.4 7.6 - - + -
93A VAL* 2.9 38.1 + - + +
94A ALA* 3.8 4.3 - - - +
95A ALA 3.2 0.2 - - - -
96A ALA* 1.3 75.3 - - - +
98A ASP* 1.3 61.0 + - - +
101A PHE* 2.8 33.9 + - + +
102A GLY 3.7 0.5 + - - -
103A SER 3.9 0.8 - - - +
104A PHE* 3.9 21.1 - - + +
107A PHE* 3.5 46.4 - - + -
126A LEU* 4.4 10.8 - - + -
134A LEU* 4.1 16.6 - - + -
185A TRP* 4.1 17.0 - - + -
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Residues in contact with ASP 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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94A ALA* 3.0 22.4 + - - +
95A ALA* 3.9 7.5 - - - +
97A ILE* 1.3 73.7 - - - +
99A ALA* 1.3 61.0 + - - +
102A GLY* 2.8 41.9 + - - +
103A SER* 3.3 19.7 - - - -
104A PHE* 3.4 8.8 + - - +
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Residues in contact with ALA 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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95A ALA 3.0 19.1 + - - +
96A ALA* 3.6 6.7 - - - +
98A ASP* 1.3 76.9 - - - +
100A ALA* 1.3 62.7 + - + +
102A GLY* 4.6 0.3 + - - -
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Residues in contact with ALA 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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96A ALA 3.0 17.1 + - - +
99A ALA* 1.3 79.9 - - + +
101A PHE* 1.3 81.5 + - + +
133A SER* 6.3 0.2 - - - -
134A LEU* 3.7 30.1 - - + +
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Residues in contact with PHE 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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97A ILE* 2.8 24.5 + - + +
100A ALA* 1.3 91.9 - - + +
102A GLY* 1.3 59.1 + - - +
103A SER 3.4 3.1 - - - +
106A GLU* 3.4 25.4 - - - +
107A PHE* 3.6 53.2 - + + +
110A LYS* 5.2 8.1 - - + -
126A LEU* 4.0 13.2 - - + -
134A LEU* 3.9 21.1 - - + -
135A ALA* 4.3 6.7 - - - -
136A ILE* 3.8 32.3 - - + -
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Residues in contact with GLY 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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97A ILE 3.7 0.4 + - - -
98A ASP* 2.8 31.4 + - - +
99A ALA 4.6 0.6 + - - -
100A ALA 3.7 0.6 - - - -
101A PHE* 1.3 75.8 - - - +
103A SER* 1.3 60.4 + - - +
106A GLU* 3.3 10.1 - - - -
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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