Contacts of the helix formed by residues 132 - 138 (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 PHE 132 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H PHE* 3.2 36.1 - - + -
84H ASN* 3.4 13.9 - - - -
86H SER* 4.6 1.8 - - - -
87H MET* 3.4 30.3 - - + -
90H ILE* 4.9 0.7 - - + -
118H ASN* 2.9 21.9 + - - +
130H GLN* 3.4 44.2 - - + -
131H CYS* 1.3 78.5 - - - +
133H ALA* 1.3 67.0 + - - +
134H ALA 3.3 2.9 - - - -
135H TRP* 2.8 38.1 + + + +
136H TYR* 2.9 41.1 + + + -
170H LEU* 4.5 4.9 - - + -
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Residues in contact with ALA 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ASN* 4.0 4.0 - - - +
131H CYS* 3.6 9.8 - - - -
132H PHE* 1.3 75.9 - - - +
134H ALA* 1.3 54.9 + - - +
136H TYR* 3.4 0.7 + - - +
137H GLY* 2.9 33.6 + - - -
144H VAL* 4.9 0.9 - - - +
170H LEU* 3.7 22.1 - - + +
212H HIS* 3.9 23.3 - - + +
241H ILE* 3.9 13.0 - - + +
271H VAL* 3.4 22.4 - - + -
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Residues in contact with ALA 134 (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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138F HIS* 3.7 30.1 - - + +
269F PHE* 3.6 19.7 - - - +
131H CYS* 5.1 3.2 - - - +
132H PHE 4.9 0.9 - - - -
133H ALA* 1.3 79.9 - - - +
135H TRP* 1.3 63.6 + - + +
137H GLY 3.6 0.2 + - - -
138H HIS* 3.5 16.5 + - - +
263H GLU* 5.7 0.7 - - - +
269H PHE 3.6 22.4 - - - +
270H GLY* 3.9 8.1 - - - -
271H VAL* 3.6 10.2 - - + +
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Residues in contact with TRP 135 (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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90F ILE* 3.6 31.4 - - + -
94F ILE* 3.8 20.2 - - + -
134F ALA 5.1 0.7 - - - -
135F TRP* 3.2 78.3 + + + +
136F TYR* 5.5 0.4 - + - -
138F HIS* 3.5 28.9 - + + -
139F CYS* 4.0 16.2 - - - -
87H MET* 4.3 15.5 - - + -
90H ILE* 3.8 24.7 - - + -
130H GLN* 4.4 7.4 - - - -
131H CYS 5.7 0.2 - - - -
132H PHE* 2.8 33.7 + + + +
134H ALA* 1.3 75.2 - - + +
136H TYR* 1.3 67.5 + - + +
138H HIS* 3.3 15.9 - - - +
139H CYS* 4.0 0.7 - - - -
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Residues in contact with TYR 136 (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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135F TRP* 5.9 0.9 - + - -
80H PHE* 5.5 0.2 - - - -
83H PHE* 4.0 19.0 - + - -
86H SER* 2.7 31.5 + - - -
90H ILE* 3.4 35.2 - - + +
93H VAL* 4.0 20.6 - - + +
94H ILE* 4.3 5.4 - - + -
132H PHE* 2.9 42.8 + + + +
135H TRP* 1.3 79.5 - - + +
137H GLY* 1.3 63.2 + - - +
138H HIS 3.1 2.3 + - - -
139H CYS* 3.1 14.4 + - - +
142H LEU* 3.6 31.1 - - + +
144H VAL* 3.6 27.6 - - + +
168H VAL* 4.1 9.4 - - + -
170H LEU* 4.2 11.9 - - + -
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Residues in contact with GLY 137 (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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268F GLN* 4.1 0.2 - - - +
269F PHE* 3.2 27.9 - - - -
133H ALA 2.9 18.1 + - - -
134H ALA 4.0 0.2 - - - -
135H TRP 3.1 0.2 - - - -
136H TYR* 1.3 77.8 - - - +
138H HIS* 1.3 49.6 + - - +
139H CYS 3.4 0.4 - - - -
144H VAL* 4.1 4.2 - - - +
241H ILE* 4.6 3.6 - - - -
242H ARG* 2.6 48.5 + - - +
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Residues in contact with HIS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F GLN* 5.4 0.4 - - - -
131F CYS 4.3 11.3 + - - -
134F ALA* 3.6 22.9 - - + +
135F TRP* 3.2 31.6 - + + +
265F GLY* 5.1 1.3 - - - -
266F TRP* 3.4 70.9 + + + +
268F GLN* 2.6 33.2 + - - +
269F PHE* 3.5 2.9 - - + -
270F GLY* 4.2 3.1 - - - -
134H ALA 3.5 10.4 + - - +
135H TRP 3.3 16.4 + - - +
136H TYR 3.1 0.2 + - - -
137H GLY* 1.3 73.2 - - - +
139H CYS* 1.3 56.9 + - - +
140H PRO* 3.6 2.3 - - - +
242H ARG* 3.2 12.1 + - - +
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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