Contacts of the helix formed by residues 132 - 138 (chain V) 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 PHE 132 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83V PHE* 3.3 35.0 - - + -
84V ASN* 3.4 13.9 - - - -
86V SER* 4.8 1.3 - - - -
87V MET* 3.6 31.0 - - + -
90V ILE* 5.2 0.7 - - + -
118V ASN* 2.9 25.4 - - - +
130V GLN* 3.5 45.3 - - + -
131V CYS* 1.3 71.8 - - - +
133V ALA* 1.3 64.6 + - - +
134V ALA 3.2 3.1 - - - -
135V TRP* 3.1 37.1 + + - +
136V TYR* 3.1 40.4 + + + -
170V LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118V ASN* 5.1 0.2 - - - +
131V CYS* 3.5 12.5 - - - -
132V PHE* 1.3 76.6 - - - +
134V ALA* 1.3 57.8 + - - +
137V GLY* 3.1 20.8 + - - -
144V VAL* 4.6 0.7 - - - +
170V LEU* 3.5 25.9 - - + +
212V HIS* 3.8 29.2 - - + -
241V ILE* 3.3 26.4 - - + +
271V VAL* 4.1 7.6 - - + -
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Residues in contact with ALA 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131V CYS* 5.2 2.0 + - - +
132V PHE 3.2 0.4 - - - -
133V ALA* 1.3 76.7 - - - +
135V TRP* 1.3 69.6 + - + +
138V HIS* 3.2 20.1 + - - +
263V GLU* 5.4 0.7 - - - +
269V PHE 3.6 24.2 - - - +
270V GLY* 3.8 16.6 - - - -
271V VAL* 4.0 10.2 - - + +
135X TRP* 5.4 0.2 - - - -
138X HIS* 4.3 13.0 - - + +
269X PHE* 3.7 17.6 - - + +
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Residues in contact with TRP 135 (chain V).
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* 4.2 12.8 - - + -
90V ILE* 4.0 17.3 - - + -
130V GLN* 4.3 10.3 - - - -
131V CYS 5.9 0.9 - - - -
132V PHE* 3.1 41.4 + + + +
134V ALA* 1.3 80.4 - - + +
136V TYR* 1.3 61.6 + - + +
138V HIS* 2.9 25.1 - - - +
139V CYS* 3.7 4.2 - - - -
269V PHE 6.0 0.2 - - - -
90X ILE* 4.1 21.8 - - + -
94X ILE* 4.2 15.5 - - + -
135X TRP* 3.2 79.9 + + + +
138X HIS* 3.4 28.6 - + - -
139X CYS* 3.7 16.4 - - - -
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Residues in contact with TYR 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V PHE* 3.9 20.5 - + - -
86V SER* 2.6 29.2 + - - -
90V ILE* 3.5 36.1 - - + +
93V VAL* 4.0 21.8 - - + +
94V ILE* 4.5 5.2 - - + -
132V PHE* 3.1 39.2 + + + +
135V TRP* 1.3 75.5 - - + +
137V GLY* 1.3 59.4 + - - +
138V HIS 2.9 10.3 + - - -
139V CYS* 3.0 15.8 + - - +
142V LEU* 3.6 31.1 - - + +
144V VAL* 3.8 25.9 - - + +
168V VAL* 4.3 17.0 - - + -
170V LEU* 4.8 1.6 - - + -
242V ARG* 4.6 0.3 - - - -
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Residues in contact with GLY 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133V ALA 3.1 22.0 + - - -
135V TRP 3.3 0.4 - - - -
136V TYR* 1.3 74.9 - - - +
138V HIS* 1.3 56.5 + - - +
144V VAL* 4.1 3.9 - - - +
241V ILE* 4.1 5.4 - - - -
242V ARG* 2.9 43.1 + - - +
269X PHE* 3.2 23.5 - - - -
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Residues in contact with HIS 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V ALA 3.2 11.3 + - - +
135V TRP* 2.9 17.7 + - - +
136V TYR 2.9 0.2 + - - -
137V GLY* 1.3 78.2 - - - +
139V CYS* 1.3 58.6 + - - +
140V PRO* 3.7 6.2 - - - +
242V ARG* 3.6 8.7 + - - +
130X GLN* 5.2 1.8 - - - -
131X CYS* 4.8 9.5 + - - +
134X ALA* 4.3 9.3 - - + +
135X TRP* 3.7 23.8 - + + +
265X GLY* 5.7 0.8 - - - -
266X TRP* 3.5 68.6 + + + +
268X GLN* 2.6 28.6 + - - +
269X PHE* 3.7 12.1 + - + +
270X GLY* 4.1 12.3 - - - -
299X ASP* 4.9 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