Contacts of the helix formed by residues 136 - 141 (chain C) in PDB entry 4CQM
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 ILE 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C SER* 1.3 76.1 + - - +
137C VAL* 1.3 73.5 + - + +
139C LEU* 3.4 25.7 + - + +
140C LYS* 3.2 28.0 + - + +
177C ALA* 3.7 10.8 - - + +
178C PRO 3.0 18.8 + - - +
179C GLY* 3.7 16.2 - - - -
180C PHE* 5.7 0.2 - - + -
228C VAL* 3.9 27.4 - - + -
230C ASP* 4.4 5.8 - - + +
233C LEU* 4.5 13.2 - - + -
234C GLN* 4.0 31.0 - - + +
237C LEU* 4.8 7.0 - - + -
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLY* 4.4 0.2 - - - -
135C SER* 3.1 13.9 - - - +
136C ILE* 1.3 82.4 - - + +
138C GLY* 1.3 61.7 + - - +
139C LEU 3.1 2.2 - - - -
141C GLY* 2.7 28.9 + - - +
142C ASN* 3.4 36.1 - - + +
145C GLN* 3.6 22.4 - - + +
148C TYR* 5.3 5.2 - - + -
149C SER* 3.1 27.4 - - - +
179C GLY 5.7 1.1 - - - +
180C PHE* 4.9 12.1 - - + -
237C LEU* 4.7 7.2 - - + -
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Residues in contact with GLY 138 (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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153B GLY 5.3 0.2 - - - +
156B VAL* 5.3 0.3 - - - +
157B GLY* 3.3 15.5 + - - -
135C SER* 2.9 17.1 + - - -
137C VAL* 1.3 78.4 - - - +
139C LEU* 1.3 57.8 + - - +
148C TYR* 6.1 0.4 - - - -
149C SER* 3.7 16.8 - - - +
152C LYS* 4.1 8.5 - - - +
153C GLY* 3.1 31.1 - - - +
156C VAL* 5.5 2.1 - - - +
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Residues in contact with LEU 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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139B LEU* 6.5 0.7 - - + -
156B VAL* 4.1 9.0 - - + +
157B GLY* 4.7 3.6 - - - -
160B ARG* 2.8 29.1 + - - -
135C SER 3.8 16.8 - - - +
136C ILE* 3.6 27.6 - - + +
137C VAL 3.1 0.4 - - - -
138C GLY* 1.3 78.0 - - - +
140C LYS* 1.3 92.8 + - + +
141C GLY 3.8 0.4 - - - -
156C VAL* 4.9 16.4 - - + -
177C ALA* 4.2 1.3 - - + -
226C VAL* 4.2 25.6 - - + -
228C VAL* 5.4 3.1 - - + -
234C GLN* 5.4 2.9 - - - +
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Residues in contact with LYS 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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160A LYS* 4.4 17.4 - - - +
161A VAL* 6.1 2.0 - - - -
261A MET* 3.1 27.1 + - - +
160B ARG* 3.4 27.1 - - - +
164B LYS* 3.0 18.2 - - - +
136C ILE* 3.2 19.9 + - + +
139C LEU* 1.3 108.8 - - + +
141C GLY* 1.3 65.8 - - - +
234C GLN* 5.3 19.4 + - + +
237C LEU* 4.0 29.4 - - + +
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Residues in contact with GLY 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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157B GLY 3.8 4.1 + - - -
160B ARG* 4.3 0.6 - - - +
161B ALA* 3.7 21.3 - - - -
164B LYS* 2.4 30.3 + - - -
137C VAL* 2.7 24.4 + - - -
139C LEU 3.8 0.4 - - - -
140C LYS* 1.3 78.5 + - - +
142C ASN* 1.3 61.4 + - - +
237C LEU* 3.5 7.6 - - - +
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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