Contacts of the helix formed by residues 138 - 144 (chain C) in PDB entry 2I6A
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 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ASN* 4.2 7.6 - - - +
16C LEU* 3.8 19.5 - - + -
40C LEU* 4.1 18.4 - - + -
121C GLY* 2.9 12.3 - - - -
136C ALA* 3.5 15.6 + - + +
137C ASN* 1.3 71.3 - - - +
139C ALA* 1.3 67.1 + - - +
140C ALA 2.9 1.4 + - - -
141C ALA* 2.7 18.9 + - + +
142C ASN* 4.0 22.2 - - + +
173C THR* 3.7 15.5 - - - +
174C VAL* 3.6 28.7 - - + -
500C 5I5 3.7 26.0 - - - +
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLN* 3.6 22.5 + - - +
119C PRO* 3.2 30.3 - - + +
120C THR 4.4 0.9 - - - +
121C GLY* 4.0 3.8 - - - -
137C ASN* 3.0 25.1 + - - +
138C LEU* 1.3 74.5 - - - +
140C ALA* 1.3 59.6 + - - +
142C ASN* 2.9 28.6 + - - +
143C CYS* 4.2 0.3 + - - -
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C CYS* 3.3 11.3 - - - +
90C ILE 3.9 14.1 - - - -
91C GLY 3.9 0.2 - - - +
115C GLN* 3.3 26.0 - - - +
118C GLN* 3.5 10.3 - - - +
119C PRO 2.9 20.1 + - - +
120C THR* 4.0 3.1 - - - -
138C LEU 2.9 2.2 + - - -
139C ALA* 1.3 73.9 - - - +
141C ALA* 1.3 55.1 + - - +
142C ASN 2.9 5.6 - - - -
143C CYS* 2.7 35.3 + - - -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 5.2 0.2 - - - +
14C ASN* 3.6 28.9 - - + +
15C PRO* 3.7 14.2 - - + +
16C LEU* 3.6 24.7 - - + -
89C CYS* 3.4 13.2 + - - +
121C GLY 4.3 2.0 - - - +
138C LEU* 2.7 22.0 + - + +
140C ALA* 1.3 71.0 - - - +
142C ASN* 1.3 57.4 + - - +
143C CYS 3.5 0.3 + - - -
144C TYR* 4.1 7.3 + - - +
171C PHE* 4.5 1.2 - - - -
174C VAL* 3.3 17.4 - - - +
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Residues in contact with ASN 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLN* 5.4 3.0 + - - +
138C LEU* 4.0 17.2 + - + +
139C ALA 2.9 15.2 + - - +
140C ALA 2.9 0.8 + - - -
141C ALA* 1.3 78.2 - - - +
143C CYS* 1.3 59.1 + - - +
144C TYR 3.4 2.8 + - - +
145C LYS* 5.3 4.2 - - - -
173C THR 3.6 12.5 + - - -
174C VAL* 3.4 34.2 + - - +
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Residues in contact with CYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C CYS* 3.4 20.4 - - - -
113C TYR* 4.6 7.9 - - + -
115C GLN* 3.8 17.7 - - + +
118C GLN* 3.8 14.8 - - + -
139C ALA 4.2 0.4 - - - -
140C ALA* 2.7 51.2 + - - -
142C ASN* 1.3 78.6 - - - +
144C TYR* 1.3 62.3 + - - +
145C LYS* 3.3 19.0 + - - +
148C LYS* 5.0 1.4 - - - +
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C MET* 3.3 27.0 - - + +
87C PHE* 4.0 3.9 - - + -
88C GLY* 3.9 32.8 - - - -
89C CYS* 4.0 13.2 - - + +
113C TYR* 4.5 5.2 - - + -
141C ALA 4.4 1.6 - - - +
142C ASN 3.4 4.3 - - - +
143C CYS* 1.3 75.2 - - - +
145C LYS* 1.3 72.0 + - - +
149C HIS* 2.9 47.0 + + + -
150C LEU* 3.1 22.9 - - + +
171C PHE* 3.7 30.3 - + + -
174C VAL* 4.2 11.5 - - + +
175C SER* 3.4 19.8 + - - -
178C SER* 3.8 16.2 - - - -
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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