Contacts of the helix formed by residues 132 - 137 (chain H) in PDB entry 1W88
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 LEU 132 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ARG* 5.1 0.4 - - - +
83H PHE* 3.3 50.0 - - + +
84H GLY* 4.1 17.3 - - - +
86H VAL 5.3 2.0 - - - +
87H TYR* 3.6 35.0 - - + +
118H PHE* 5.3 1.2 - - - -
130H ASP* 3.5 22.3 + - + +
131H SER* 1.3 78.4 - - - +
133H GLU* 1.3 64.2 + - - +
134H GLY 3.1 3.1 - - - +
135H LEU* 3.1 37.0 + - + +
136H VAL* 3.7 6.6 + - - +
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Residues in contact with GLU 133 (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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83H PHE* 4.5 1.8 - - - -
118H PHE* 4.7 4.0 - - - -
131H SER* 3.1 31.4 + - - -
132H LEU* 1.3 75.1 - - - +
134H GLY* 1.3 69.0 + - - +
136H VAL* 3.4 12.8 - - + +
137H ALA* 3.1 27.9 + - - +
144H VAL* 5.0 0.3 - - - +
146H ILE* 3.9 9.0 - - + -
170H LEU* 3.7 24.7 - - + +
209H TYR* 2.3 50.2 + - + +
238H VAL* 4.6 5.6 - - + -
260H GLN* 4.9 0.2 - - - +
262H ALA* 3.9 7.6 + - - +
267H GLY* 3.5 9.9 - - - -
268H ILE* 4.4 9.4 - - + -
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Residues in contact with GLY 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 GLN* 3.0 24.1 + - - +
132H LEU* 3.1 3.4 - - - +
133H GLU* 1.3 84.1 - - - +
135H LEU* 1.3 56.3 + - - +
137H ALA* 4.1 2.3 + - - +
138H GLN* 3.3 24.8 + - - +
267H GLY* 3.4 28.3 - - - +
268H ILE* 4.1 3.9 - - - +
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Residues in contact with LEU 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 MET* 4.9 4.9 - - - -
135F LEU* 3.5 58.5 - - + +
138F GLN* 3.7 19.3 - - + +
87H TYR* 3.8 30.5 - - + +
90H MET* 4.1 29.1 - - - +
132H LEU* 3.1 32.5 + - + +
134H GLY* 1.3 74.1 - - - +
136H VAL* 1.3 65.3 + - + +
137H ALA 3.2 2.0 - - - -
138H GLN* 3.2 11.8 + - - +
139H GLN* 4.2 2.4 + - - +
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Residues in contact with VAL 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PHE* 3.7 30.3 - - + -
90H MET* 4.6 10.3 - - + -
93H ILE* 5.3 2.2 - - + -
94H CYS* 4.2 21.3 - - - -
132H LEU 3.9 2.2 - - - +
133H GLU* 3.4 25.1 - - - +
135H LEU* 1.3 69.8 - - - +
137H ALA* 1.3 61.0 + - - +
138H GLN 3.0 8.9 + - - -
139H GLN* 3.2 19.6 + - - +
142H LEU* 3.6 21.8 - - + +
144H VAL* 3.9 23.1 - - + +
168H ILE* 4.4 10.5 - - + -
170H LEU* 4.7 1.8 - - + -
239H GLN* 5.7 0.2 - - - +
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Residues in contact with ALA 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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265F GLN* 2.8 22.4 + - - +
133H GLU 3.1 19.6 + - - +
134H GLY 4.3 3.1 - - - +
135H LEU 3.2 0.2 - - - -
136H VAL* 1.3 77.5 - - - +
138H GLN* 1.3 58.0 + - + +
139H GLN 3.3 0.7 - - - -
144H VAL* 4.2 10.5 - - + -
238H VAL* 4.8 3.4 - - + +
239H GLN* 3.1 34.5 + - + +
268H ILE* 3.8 22.9 - - + -
271H ASN* 5.1 3.7 + - - +
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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