Contacts of the helix formed by residues 89 - 102 (chain A) in PDB entry 3OJW
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 GLY 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A SER* 2.9 16.0 + - - -
87A GLN 3.5 0.4 - - - -
88A THR* 1.3 77.5 - - - +
90A THR* 1.3 64.2 + - - +
92A GLU* 3.8 11.5 - - - +
93A GLU* 3.1 23.9 + - - +
452A GLN* 3.4 18.9 - - - +
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Residues in contact with THR 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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88A THR* 3.4 5.2 + - - -
89A GLY* 1.3 74.6 - - - +
91A ALA* 1.3 61.2 + - - +
93A GLU* 3.3 5.4 + - - +
94A PHE* 3.2 31.7 + - + -
173A LEU* 3.5 15.3 - - + -
212A LEU* 3.6 19.3 - - + -
382A ARG* 6.1 2.9 - - - +
751A FMN 2.8 40.4 + - - +
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Residues in contact with ALA 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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84A TYR* 4.0 1.6 - - - -
85A GLY 3.2 22.9 - - - +
86A SER* 3.5 3.6 - - - -
90A THR* 1.3 69.9 - - - +
92A GLU* 1.3 67.6 + - - +
94A PHE* 3.2 6.4 + - - +
95A ALA* 2.9 22.9 + - - +
136A ALA* 3.7 12.5 - - - +
138A ALA 4.5 0.4 - - - +
173A LEU* 3.4 30.0 - - + +
751A FMN 2.6 20.4 + - - +
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Residues in contact with GLU 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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84A TYR* 3.2 54.8 + - + -
86A SER* 3.4 12.0 + - - +
89A GLY* 3.8 15.4 - - - +
90A THR 3.3 0.8 - - - -
91A ALA* 1.3 78.5 - - - +
93A GLU* 1.3 56.9 + - - +
95A ALA* 3.2 4.7 + - - +
96A ASN* 2.9 45.3 + - - +
357A LYS* 6.0 1.2 - - - -
450A ARG* 5.7 9.0 - - - +
452A GLN* 4.6 8.3 + - - +
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Residues in contact with GLU 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 GLY 3.1 14.9 + - - +
90A THR* 3.7 4.8 - - - +
92A GLU* 1.3 75.6 - - - +
94A PHE* 1.3 75.8 + - - +
96A ASN* 3.1 15.3 + - + +
97A ARG* 2.8 68.6 + - - +
382A ARG* 3.9 18.1 + - - +
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Residues in contact with PHE 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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90A THR* 3.2 19.2 + - + -
91A ALA* 3.2 7.2 + - - +
93A GLU* 1.3 87.9 - - - +
95A ALA* 1.3 57.1 + - - +
97A ARG* 3.1 17.8 + - - +
98A LEU* 2.9 35.5 + - + +
136A ALA* 4.6 7.4 - - + -
171A PHE* 4.0 21.8 - + + -
173A LEU* 3.8 29.4 - - + -
212A LEU* 3.9 25.4 - - + -
213A GLU* 3.8 11.2 - - - -
216A PHE* 3.4 52.7 - + + -
382A ARG* 5.3 1.1 - - - -
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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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82A VAL* 3.7 33.0 - - + +
84A TYR* 3.8 27.6 - - + -
91A ALA 2.9 12.7 + - - +
92A GLU 3.4 9.0 - - - +
94A PHE* 1.3 76.0 - - - +
96A ASN* 1.3 58.1 + - - +
98A LEU* 3.9 0.7 - - - +
99A SER* 2.9 31.4 + - - -
111A SER* 3.8 5.0 - - - -
136A ALA* 4.5 4.6 - - + +
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Residues in contact with ASN 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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84A TYR* 4.9 0.9 - - - -
92A GLU* 2.9 37.6 + - - +
93A GLU* 3.1 18.4 + - + +
95A ALA* 1.3 77.1 - - - +
97A ARG* 1.3 62.0 + - - +
99A SER* 3.5 2.8 + - - -
100A LYS* 3.0 23.9 + - - +
111A SER* 3.0 25.1 + - - -
357A LYS* 3.4 34.5 + - + +
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Residues in contact with ARG 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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93A GLU* 2.8 47.5 + - - +
94A PHE* 3.1 16.1 + - - +
96A ASN* 1.3 77.4 - - - +
98A LEU* 1.3 56.7 + - - +
100A LYS* 3.3 13.6 + - + +
101A ASP* 2.9 33.8 + - - +
213A GLU* 2.8 41.0 + - - -
216A PHE* 3.6 22.1 - - + -
217A ILE* 3.7 12.3 - - - +
220A ARG* 3.8 25.1 - - - +
382A ARG* 3.2 8.8 - - - +
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Residues in contact with LEU 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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80A ILE* 5.7 0.7 - - - +
82A VAL* 4.3 17.6 - - + +
94A PHE* 2.9 21.2 + - + +
95A ALA* 3.9 3.6 - - - +
97A ARG* 1.3 72.5 - - - +
99A SER* 1.3 67.0 + - - +
101A ASP* 3.1 24.2 + - - +
102A ALA* 3.4 1.2 + - - +
134A VAL* 4.3 18.4 - - + -
136A ALA* 5.4 4.7 - - + -
171A PHE* 5.4 2.9 - - + -
216A PHE* 3.8 27.4 - - + -
219A TRP* 3.9 27.4 - - + -
220A ARG* 4.0 7.6 - - + -
223A PHE* 4.4 6.5 - - + -
224A TRP* 3.2 35.2 - - + +
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Residues in contact with SER 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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80A ILE* 5.8 0.7 - - - -
82A VAL* 4.1 8.8 - - - +
95A ALA 2.9 19.3 + - - -
96A ASN* 3.6 4.9 - - - -
98A LEU* 1.3 76.1 - - - +
100A LYS* 1.3 63.0 + - - +
102A ALA* 3.3 20.3 - - - +
103A HIS* 4.5 0.7 + - - +
109A GLY* 3.1 14.6 + - - +
110A MET* 3.0 32.2 + - - -
111A SER* 3.4 17.8 + - - -
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Residues in contact with LYS 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 ASN 3.0 17.7 + - - +
97A ARG* 3.5 13.0 - - + +
98A LEU 3.2 0.2 - - - -
99A SER* 1.3 78.2 - - - +
101A ASP* 1.3 64.1 + - - +
102A ALA 3.3 0.5 + - - -
103A HIS* 3.3 21.7 + - + +
104A ARG* 4.3 3.3 + - - +
240A SER 5.4 6.4 + - - -
241A SER* 5.7 6.6 - - - -
243A ARG 6.2 0.4 - - - -
244A GLN* 3.5 39.7 + - - +
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Residues in contact with ASP 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 ARG 2.9 21.5 + - - +
98A LEU* 3.1 9.3 + - - +
100A LYS* 1.3 78.0 - - - +
102A ALA* 1.3 55.2 - - - +
104A ARG* 2.7 62.1 + - - +
105A TYR* 3.8 5.5 + - - -
220A ARG* 2.8 40.8 + - - -
224A TRP* 2.9 34.7 + - + +
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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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80A ILE* 4.2 12.6 - - + -
98A LEU 3.4 3.4 + - - +
99A SER* 3.3 16.2 + - - +
101A ASP* 1.3 77.6 - - - +
103A HIS* 1.3 56.5 + - - +
105A TYR* 3.1 14.4 + - - +
107A MET* 3.0 30.8 + - - +
108A ARG 4.0 2.5 - - - -
109A GLY* 3.6 23.8 - - - +
224A TRP* 3.7 21.7 - - + -
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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