Contacts of the helix formed by residues 123 - 128 (chain C) in PDB entry 2GER
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 ASN 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.3 7.9 - - - +
122C THR* 1.3 76.5 + - - +
124C THR* 1.3 61.4 + - - +
125C PRO* 3.2 16.9 - - + +
126C VAL* 2.8 30.3 - - - +
131C GLY* 3.0 13.2 - - - -
132C ALA* 2.9 49.2 + - - +
174C SER* 3.1 30.4 + - - +
175C GLY 4.4 7.2 - - - +
178C PRO* 4.2 8.3 - - + +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 6.1 1.3 - - - +
11C LEU* 3.3 18.9 - - + +
14C ALA* 3.8 2.0 - - + +
123C ASN* 1.3 67.9 - - - +
125C PRO* 1.4 59.3 - - - +
126C VAL* 2.5 20.9 + - - +
127C VAL* 2.9 34.4 + - + +
178C PRO* 5.6 4.3 - - - +
182C PHE* 6.1 5.6 - - - -
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Residues in contact with PRO 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASN* 3.2 24.9 - - + +
124C THR* 1.4 88.9 - - - +
126C VAL* 1.3 60.7 + - - +
127C VAL* 2.8 9.6 - - + +
128C VAL* 2.8 24.0 + - + +
130C GLU* 3.0 30.5 - - + +
131C GLY* 3.9 0.2 - - - -
178C PRO* 4.4 17.0 - - + -
182C PHE* 6.3 2.5 - - + -
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.5 7.2 - - + -
14C ALA* 3.4 32.1 - - + +
15C LEU* 4.4 12.1 - - + +
18C GLY* 4.1 1.7 - - - -
122C THR* 3.5 23.8 - - + +
123C ASN* 2.8 33.0 + - - +
124C THR 2.5 16.4 + - - +
125C PRO* 1.3 69.8 - - - +
127C VAL* 1.3 51.9 + - - +
128C VAL 2.4 30.3 + - - +
131C GLY* 4.1 7.6 - - - +
133C THR* 3.9 9.2 - - + -
156C VAL* 3.5 19.2 - - + +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PHE* 6.1 2.2 - - + -
14C ALA* 3.4 32.3 - - + -
17C LYS* 4.3 32.5 - - + +
18C GLY* 4.8 6.1 - - - +
21C ALA* 6.1 1.0 - - - +
124C THR* 2.9 26.9 + - + +
125C PRO* 4.4 3.6 - - + -
126C VAL* 1.3 76.4 - - - +
128C VAL* 1.3 65.9 + - + +
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Residues in contact with VAL 128 (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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18C GLY* 5.8 0.7 - - - -
125C PRO* 2.8 10.1 + - + +
126C VAL* 2.4 26.2 + - - +
127C VAL* 1.3 87.4 - - + +
129C ARG* 1.3 70.2 + - + +
130C GLU* 2.7 32.1 + - + +
156C VAL* 3.2 7.7 - - - +
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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