Contacts of the helix formed by residues 132 - 140 (chain C) in PDB entry 2Q41
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 GLY 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C GLY 3.5 8.2 + - - -
131C ASP* 1.3 80.4 + - - +
133C GLY* 1.3 51.8 + - - +
134C VAL* 3.2 3.3 - - - +
135C LEU* 2.8 20.1 + - - +
136C ARG* 2.6 31.7 + - - +
149C MSE 6.0 0.2 - - - -
167C VAL 3.3 12.3 - - - -
170C GLY* 3.3 7.0 - - - -
171C TYR* 3.6 13.4 + - - -
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Residues in contact with GLY 133 (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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107C GLN* 3.1 23.6 - - - -
131C ASP* 3.0 10.2 + - - -
132C GLY* 1.3 76.8 - - - +
134C VAL* 1.3 51.3 + - - +
136C ARG* 2.9 26.2 + - - +
137C GLU* 2.8 32.1 + - - +
167C VAL* 3.6 10.0 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 4.7 1.1 - - + -
107C GLN* 3.2 34.6 - - + +
110C ILE* 3.8 13.2 - - + -
111C THR* 3.1 22.7 - - - +
126C VAL* 4.5 13.7 - - + -
129C GLY 5.8 1.1 - - - +
131C ASP* 4.7 2.2 - - - +
132C GLY* 3.2 0.9 - - - +
133C GLY* 1.3 74.6 - - - +
135C LEU* 1.3 63.2 + - - +
137C GLU* 3.0 12.9 + - - +
138C VAL* 3.0 19.3 + - + +
149C MSE 5.2 4.7 - - + -
199C ILE* 4.4 17.3 - - + -
201C ASP* 4.1 26.9 - - + +
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Residues in contact with LEU 135 (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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126C VAL* 4.7 8.7 - - + -
132C GLY* 2.8 19.4 + - - +
134C VAL* 1.3 80.2 - - - +
136C ARG* 1.3 57.7 + - - +
138C VAL* 3.5 7.3 + - - +
139C ALA* 3.4 17.7 + - - +
147C ILE* 3.2 36.8 - - + +
149C MSE 4.1 29.0 - - + +
170C GLY* 3.3 33.0 - - - +
171C TYR* 3.5 29.4 - - + +
173C ASP* 5.8 0.2 - - - +
176C VAL* 3.8 14.0 - - + +
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Residues in contact with ARG 136 (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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103C GLU* 4.5 11.7 + - - +
104C CYS* 5.2 5.3 - - - +
107C GLN* 2.8 33.3 + - - +
132C GLY 2.6 13.9 + - - +
133C GLY* 2.9 17.0 + - - +
135C LEU* 1.3 72.7 - - - +
137C GLU* 1.3 83.2 + - - +
139C ALA* 3.1 21.6 + - - +
140C ARG* 3.5 16.0 + - + +
166C ASP* 2.7 44.4 + - - +
169C ILE* 3.7 30.5 - - + -
170C GLY* 3.7 6.0 - - - -
304C ASN* 5.8 5.5 - - + +
308C LYS* 6.0 3.0 - - - +
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Residues in contact with GLU 137 (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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107C GLN* 3.6 26.7 - - + +
108C GLU* 3.5 19.0 - - + +
111C THR* 3.4 20.0 - - - +
112C HIS* 2.6 42.6 + - - -
133C GLY 2.8 17.7 + - - +
134C VAL 3.0 9.2 + - - +
136C ARG* 1.3 92.9 + - - +
138C VAL* 1.3 61.9 + - - +
140C ARG* 2.5 51.9 + - - +
141C HIS* 3.7 0.3 - - - -
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Residues in contact with VAL 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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111C THR* 3.8 19.7 - - + +
115C LEU* 4.2 9.2 - - + -
124C VAL* 3.7 17.9 - - + -
126C VAL* 4.4 14.4 - - + -
134C VAL* 3.0 16.0 + - + +
135C LEU* 3.7 5.6 - - - +
136C ARG 3.2 0.4 - - - -
137C GLU* 1.3 75.3 - - - +
139C ALA* 1.3 58.5 - - - +
141C HIS* 2.9 31.9 + - - +
144C ILE* 4.1 6.1 - - + +
147C ILE* 3.2 32.3 - - + -
199C ILE* 4.3 15.9 - - + -
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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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135C LEU 3.4 9.1 + - - +
136C ARG* 3.1 17.6 + - + +
138C VAL* 1.3 78.4 - - - +
140C ARG* 1.3 60.7 + - - +
141C HIS 3.0 4.2 + - - +
142C ALA* 5.1 0.5 - - - -
147C ILE* 3.9 5.6 - - + +
170C GLY* 6.2 0.2 - - - -
173C ASP* 3.6 27.1 - - + +
175C ARG* 3.0 23.8 + - - +
304C ASN* 4.7 9.7 + - - +
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Residues in contact with ARG 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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108C GLU* 4.7 7.0 + - - -
112C HIS* 3.6 14.4 - - + -
136C ARG* 4.0 15.3 + - + +
137C GLU* 2.5 51.5 + - - +
138C VAL 3.0 0.8 + - - -
139C ALA* 1.3 78.0 - - - +
141C HIS* 1.3 60.3 + - + +
142C ALA* 3.3 4.7 + - - +
296C ILE* 4.8 8.8 - - + +
300C SER* 3.8 8.3 - - - +
301C SER* 3.1 40.2 + - - +
304C ASN* 3.8 29.1 + - + +
305C GLY 2.9 23.8 + - - -
306C PRO 3.6 14.6 + - - -
307C LEU* 3.8 22.1 - - - +
308C LYS* 6.0 1.4 - - - +
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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