Contacts of the helix formed by residues 89 - 96 (chain H) in PDB entry 3EXF
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H GLU* 4.0 7.9 - - + +
60H MET* 4.1 9.2 - - - +
63H ALA* 3.5 27.1 - - + -
80H PHE* 3.7 23.3 - - + -
86H SER* 2.9 9.1 + - - +
88H GLN* 1.3 77.6 - - - +
90H ILE* 1.3 53.4 + - - +
91H ASP 2.9 3.8 - - - -
92H GLN* 2.4 30.6 + - - +
93H VAL* 3.1 10.2 + - + +
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Residues in contact with ILE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F MET* 3.9 21.3 - - + +
90F ILE* 3.9 22.9 - - + -
135F TRP* 4.2 15.3 - - + -
86H SER* 2.9 10.1 + - - +
87H MET* 4.0 9.4 - - - +
88H GLN 3.5 1.0 - - - -
89H ALA* 1.3 77.7 - - - +
91H ASP* 1.3 64.8 + - - +
93H VAL* 4.2 5.4 - - - -
94H ILE* 3.0 29.6 + - + +
132H PHE* 4.9 2.2 - - + -
135H TRP* 3.8 31.4 - - + -
136H TYR* 3.4 43.7 - - + +
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Residues in contact with ASP 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASN 3.5 14.4 - - - +
87F MET* 3.5 14.6 + - + +
88F GLN* 3.8 37.7 - - + +
137G ILE* 3.4 23.5 - - - +
140G ALA* 4.5 7.1 - - - +
60H MET* 4.2 11.3 - - + +
88H GLN 4.8 0.4 + - - -
89H ALA 2.9 1.2 - - - +
90H ILE* 1.3 84.5 - - - +
92H GLN* 1.3 61.8 + - - +
95H ASN* 3.2 44.4 + - - +
96H SER* 4.3 0.7 + - - -
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Residues in contact with GLN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G ALA* 2.8 33.5 + - + +
143G PRO* 3.7 14.1 - - - +
144G LEU* 3.6 9.6 - - - +
174G GLN* 3.3 16.2 + - - -
60H MET* 3.9 28.7 - - - +
63H ALA* 4.2 15.0 - - + -
64H GLY* 3.8 10.6 - - - -
67H VAL* 4.3 6.6 - - + +
89H ALA 2.4 25.3 + - - +
91H ASP* 1.3 70.1 - - - +
93H VAL* 1.3 60.7 + - - +
96H SER* 2.9 34.7 + - - -
97H ALA* 3.1 22.3 + - - +
114H PHE* 6.3 0.2 - - + -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ALA* 5.7 0.2 - - + -
80H PHE* 4.6 11.4 - - + -
86H SER 5.3 0.2 - - - +
89H ALA* 3.1 13.4 + - + +
90H ILE* 3.2 13.2 + - - +
92H GLN* 1.3 78.2 - - + +
94H ILE* 1.3 60.5 + - + +
97H ALA* 3.1 10.6 - - - +
98H ALA* 3.0 25.8 + - - +
114H PHE* 3.7 43.1 - - + -
136H TYR* 4.0 26.9 - - + +
142H LEU* 4.1 16.2 - - + -
168H VAL* 4.4 3.6 - - + -
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Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F MET* 4.1 9.2 - - + -
130F GLN* 3.6 16.4 - - - +
135F TRP* 4.0 22.9 - - + -
90H ILE* 3.0 17.9 + - + +
93H VAL* 1.3 84.9 - - + +
95H ASN* 1.3 64.0 + - - +
96H SER 3.5 0.2 - - - -
98H ALA* 3.4 21.1 + - + +
99H LYS* 3.6 35.2 + - - +
136H TYR* 4.3 7.4 - - + -
139H CYS* 3.3 35.2 - - + -
142H LEU* 3.6 22.7 - - + -
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Residues in contact with ASN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ASN* 4.0 4.5 + - - +
87F MET* 3.0 29.3 - - - +
127F GLN* 3.2 38.9 + - + +
130F GLN* 4.1 0.7 - - - +
137G ILE* 3.5 31.9 - - + +
91H ASP* 3.2 31.1 + - - +
94H ILE* 1.3 77.3 - - - +
96H SER* 1.3 63.6 + - - +
99H LYS* 3.1 36.1 + - - +
103H MET* 4.4 1.6 - - - +
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Residues in contact with SER 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F GLN* 5.1 2.6 + - - +
135G ASN* 5.8 0.2 - - - -
137G ILE* 6.1 0.5 - - - +
140G ALA* 4.8 7.4 - - - +
144G LEU* 4.2 25.0 - - - +
67H VAL* 4.3 5.6 - - - +
71H MET* 5.2 2.9 - - - +
91H ASP* 4.3 2.1 + - - -
92H GLN* 2.9 36.0 + - - -
95H ASN* 1.3 81.9 - - - +
97H ALA* 1.3 66.2 + - - +
99H LYS 4.7 0.4 - - - -
100H THR* 2.5 29.2 + - - -
110H VAL* 4.8 0.5 - - - +
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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