Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 2W5X
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A THR* 1.3 91.2 + - - +
84A SEP 1.3 70.9 + - - +
85A ALA 3.4 2.7 + - - -
86A SER 3.1 12.3 + - - -
87A GLY* 3.1 8.7 + - - -
99A ASN* 3.2 19.4 + - + +
100A ALA* 3.1 31.6 + - - +
148A ARG* 2.9 27.7 + - - +
302A HIS* 4.4 3.0 - - - -
337A HIS* 3.7 11.4 - - + +
325B TYR* 4.9 5.6 - - + -
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Residues in contact with SEP 84 (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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43A ASP* 3.5 8.8 + - - +
83A ASP* 1.3 80.2 - - - +
85A ALA* 1.3 57.3 + - - -
87A GLY 3.9 0.8 - - - -
88A ALA* 3.1 30.1 + - - +
135A GLU* 3.6 12.5 + - - -
136A ALA* 4.0 11.4 - - - +
137A THR* 4.2 3.8 + - - -
148A ARG* 2.6 54.4 + - - -
259A ASP* 2.6 17.8 + - - -
260A TRP* 5.2 2.8 + - - -
301A ASP* 3.4 13.6 - - - +
337A HIS* 3.1 13.9 + - - -
1377A ZN 1.9 41.8 - - - -
1378A ZN 2.0 30.3 - - - -
1379A MG 4.4 0.4 - - - -
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Residues in contact with ALA 85 (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 ASP* 3.1 6.7 + - - +
84A SEP 1.3 77.4 + - - +
86A SER* 1.3 62.1 + - - +
88A ALA 3.4 0.3 + - - -
89A THR* 3.0 32.9 + - - -
100A ALA* 3.5 26.5 - - - +
101A ALA 3.1 18.2 - - - +
102A ILE* 3.6 15.0 - - + -
136A ALA* 3.9 9.0 - - + +
140A SER* 3.5 2.9 + - - -
148A ARG* 4.1 7.0 - - + -
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Residues in contact with SER 86 (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 SER* 3.5 4.4 - - - -
82A THR* 2.8 24.7 + - - -
83A ASP* 3.1 4.1 + - - -
85A ALA* 1.3 78.1 - - - +
87A GLY* 1.3 56.4 + - - +
89A THR* 3.8 0.7 - - - -
90A ALA* 3.0 30.0 + - - +
95A ILE 4.9 0.5 - - - +
97A THR* 3.3 43.0 + - - +
98A TYR 3.4 15.7 - - - -
99A ASN* 2.9 15.6 + - - -
100A ALA 4.3 0.2 - - - +
101A ALA 3.7 0.8 + - - -
360A ASN* 4.8 0.6 + - - -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 3.7 8.7 - - - -
83A ASP 3.1 15.4 + - - -
84A SEP 4.0 0.9 - - - -
85A ALA 3.2 0.2 - - - -
86A SER* 1.3 81.9 + - - +
88A ALA* 1.3 58.1 + - - +
90A ALA* 3.5 13.7 - - - +
91A PHE* 3.7 18.9 - - - -
301A ASP* 4.4 18.6 - - - -
360A ASN* 4.2 12.5 + - - -
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Residues in contact with ALA 88 (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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84A SEP 3.1 20.8 + - - +
87A GLY* 1.3 74.6 - - - +
89A THR* 1.3 61.7 + - - +
90A ALA 3.2 1.6 - - - -
91A PHE* 3.2 13.5 + - + +
92A SER* 2.9 29.3 + - - -
137A THR* 4.0 27.8 - - + +
140A SER* 3.8 19.1 - - - +
141A PHE* 4.1 5.3 - - + -
301A ASP* 4.7 3.3 - - + +
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Residues in contact with THR 89 (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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85A ALA 3.0 22.1 + - - -
86A SER 3.9 3.8 - - - -
88A ALA* 1.3 73.9 - - - +
90A ALA* 1.3 59.3 + - - +
92A SER* 3.6 7.2 - - - -
93A CYS* 2.8 42.2 + - + +
94A GLY 3.5 0.5 + - - -
95A ILE* 4.2 7.2 - - + +
97A THR* 3.9 22.4 - - + -
101A ALA 3.3 4.2 + - - -
103A GLY* 3.0 38.7 + - - +
104A VAL 4.0 6.7 - - - +
140A SER* 3.3 8.2 + - - -
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Residues in contact with ALA 90 (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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86A SER 3.0 14.9 + - - +
87A GLY 3.5 3.8 - - - +
89A THR* 1.3 77.2 - - - +
91A PHE* 1.3 57.6 + - - +
94A GLY* 3.0 26.9 + - - -
95A ILE 3.3 19.4 + - - +
96A LYS* 5.4 2.2 - - + -
360A ASN* 3.4 39.7 - - + +
361A ASN* 3.3 16.6 - - + +
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Residues in contact with PHE 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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39A LEU* 4.5 5.2 - - + +
41A ILE* 3.9 25.8 - - + -
72A ILE* 3.7 20.6 - - + -
87A GLY 3.7 16.2 - - - -
88A ALA* 3.2 10.8 + - - +
90A ALA* 1.3 77.9 - - - +
92A SER* 1.3 59.5 + - - +
114A ILE* 5.1 1.9 - - - +
141A PHE* 4.1 11.7 - - + -
299A THR* 3.8 13.9 - - + -
300A SER 3.4 27.8 - - - -
301A ASP* 4.0 15.7 - - + -
360A ASN* 3.5 30.3 - - + -
363A ILE* 3.8 28.7 - - + +
364A PHE* 3.2 28.1 + - - +
367A ILE* 5.5 2.3 - - - +
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Residues in contact with SER 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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88A ALA 2.9 16.9 + - - -
89A THR* 3.6 5.9 - - - -
91A PHE* 1.3 78.2 - - - +
93A CYS* 1.3 67.9 + - - +
113A SER* 3.1 3.7 - - - -
114A ILE* 2.7 32.2 + - - -
140A SER 2.7 28.4 + - - -
141A PHE* 3.6 32.1 - - - -
364A PHE* 3.2 5.8 - - - -
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Residues in contact with CYS 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 THR* 2.8 19.4 + - + +
92A SER* 1.3 88.0 - - - +
94A GLY* 1.3 64.1 + - - +
95A ILE* 3.3 10.3 + - + +
103A GLY* 3.9 22.4 - - - -
111A VAL* 3.7 34.1 - - + +
112A LYS 3.9 6.1 - - - +
113A SER* 3.7 22.2 - - - -
140A SER 4.5 0.4 - - - -
144A HIS* 4.9 0.7 - - - -
364A PHE* 3.6 19.5 - - - -
365A HIS* 5.5 0.3 - - - -
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Residues in contact with GLY 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 THR 3.5 0.2 + - - -
90A ALA 3.0 17.7 + - - -
93A CYS* 1.3 78.7 - - - +
95A ILE* 1.3 61.7 + - - +
361A ASN* 3.0 21.7 + - - -
364A PHE* 3.3 25.8 - - - -
365A HIS* 3.0 20.4 + - - -
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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