Contacts of the helix formed by residues 89 - 96 (chain X) in PDB entry 3EXG
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 ALA 89 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59X GLU* 3.7 15.7 - - + +
60X MET* 4.1 7.4 - - - +
63X ALA* 3.5 28.9 - - + -
80X PHE* 3.7 17.3 - - + -
86X SER 2.7 13.6 + - - +
88X GLN* 1.3 74.6 - - - +
90X ILE* 1.3 66.4 + - - +
91X ASP 3.1 3.8 - - - -
92X GLN* 3.0 15.2 + - - +
93X VAL* 3.2 11.9 + - - +
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Residues in contact with ILE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87V MET* 4.0 33.4 - - + +
90V ILE* 4.3 8.1 - - + -
135V TRP* 4.1 12.3 - - + -
86X SER* 2.8 9.6 + - - +
87X MET* 4.2 11.2 - - + +
88X GLN 3.4 2.8 - - - -
89X ALA* 1.3 79.0 - - - +
91X ASP* 1.3 59.6 + - - +
93X VAL* 3.7 4.7 - - + -
94X ILE* 2.9 38.2 + - + +
132X PHE* 5.4 0.4 - - + -
135X TRP* 4.0 28.5 - - + -
136X TYR* 3.4 42.8 - - + +
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Residues in contact with ASP 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V ASN 4.6 1.6 - - - +
85V PHE* 5.8 0.5 - - - -
87V MET* 3.6 21.7 + - + +
88V GLN* 4.1 25.6 + - + +
137W ILE* 3.5 34.5 - - - +
140W ALA* 4.0 13.7 - - - +
60X MET* 4.4 8.5 - - + +
88X GLN 5.0 0.8 + - - +
89X ALA 3.0 1.0 + - - -
90X ILE* 1.3 85.0 - - - +
92X GLN* 1.3 58.6 + - - +
95X ASN* 2.8 56.3 + - - +
96X SER* 3.8 0.7 + - - -
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Residues in contact with GLN 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140W ALA* 3.5 25.9 + - - +
143W PRO* 3.9 8.9 - - - +
144W LEU* 3.8 9.0 - - - +
174W GLN* 3.3 24.4 + - - -
60X MET* 3.5 30.6 + - - +
63X ALA* 4.2 7.6 - - + -
64X GLY* 3.6 19.2 - - - +
67X VAL* 4.2 6.6 - - + +
89X ALA 3.0 8.0 + - - +
91X ASP* 1.3 77.4 + - - +
93X VAL* 1.3 63.5 + - + +
96X SER* 3.1 42.6 + - - -
97X ALA* 3.2 9.5 + - - +
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Residues in contact with VAL 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X PHE* 4.7 7.9 - - + -
89X ALA* 3.2 15.5 + - + +
90X ILE* 3.3 10.1 + - - +
92X GLN* 1.3 77.9 - - + +
94X ILE* 1.3 58.3 + - + +
97X ALA* 3.1 6.9 - - - +
98X ALA* 2.9 26.9 + - - +
114X PHE* 3.6 48.0 - - + -
136X TYR* 4.0 31.9 - - + +
142X LEU* 4.0 16.8 - - + +
168X VAL* 4.6 1.8 - - + -
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Residues in contact with ILE 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V MET* 4.1 12.6 - - - -
130V GLN* 3.7 26.5 - - - +
135V TRP* 4.2 10.8 - - + -
90X ILE* 2.9 29.1 + - + +
93X VAL* 1.3 80.9 - - - +
95X ASN* 1.3 60.5 + - - +
96X SER 3.5 0.2 - - - -
98X ALA* 3.4 11.0 - - + +
99X LYS* 3.4 28.3 + - - +
136X TYR* 4.4 9.2 - - + -
139X CYS* 3.5 35.2 - - + -
142X LEU* 4.2 17.9 - - + -
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Residues in contact with ASN 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V ASN* 4.6 0.4 + - - +
87V MET* 2.7 33.1 - - - +
127V GLN* 2.6 49.5 + - - +
137W ILE* 3.7 18.6 - - + +
91X ASP* 2.8 31.8 + - - +
94X ILE* 1.3 74.5 - - - +
96X SER* 1.3 63.7 + - - +
99X LYS* 3.0 36.2 + - - +
103X MET* 4.3 7.4 - - - +
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Residues in contact with SER 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V GLN* 4.9 1.8 + - - +
135W ASN* 5.6 0.7 + - - -
140W ALA* 4.5 9.0 - - - +
144W LEU* 4.0 18.0 - - - +
67X VAL* 4.0 17.3 - - - +
71X MET* 4.9 3.4 - - - +
91X ASP* 3.8 1.1 + - - -
92X GLN* 3.1 35.5 + - - -
95X ASN* 1.3 81.1 + - - +
97X ALA* 1.3 63.1 + - - +
99X LYS 4.8 0.4 - - - -
100X THR* 2.7 27.4 + - - +
110X VAL* 4.0 5.4 - - - +
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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