Contacts of the helix formed by residues 2112 - 2123 (chain C) in PDB entry 5G1N
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 PRO2112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2081C LEU 3.6 6.1 - - - +
2082C LYS* 4.2 15.9 - - + +
2088C HIS* 3.7 16.6 - - + +
2110C ARG 3.5 8.5 - - - +
2111C MET* 1.3 103.2 - - + +
2113C PRO* 1.3 66.7 - - + +
2114C THR* 3.1 11.4 - - - +
2115C VAL* 2.8 29.8 + - + +
2116C ARG* 2.9 10.2 + - - -
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Residues in contact with PRO2113 (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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2111C MET 3.7 1.2 - - - -
2112C PRO* 1.3 85.5 - - + +
2114C THR* 1.3 57.4 + - - +
2116C ARG* 3.7 28.9 - - + +
2117C ALA* 2.6 37.5 + - - +
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Residues in contact with THR2114 (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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2112C PRO* 4.3 10.6 - - - +
2113C PRO* 1.3 78.9 - - - +
2115C VAL* 1.3 70.0 + - + +
2117C ALA* 3.8 4.1 - - - +
2118C PHE* 3.1 23.6 + - - +
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Residues in contact with VAL2115 (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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2088C HIS* 3.8 37.2 - - + +
2091C ALA* 4.3 6.5 - - + -
2092C CYS* 3.9 22.2 - - - -
2111C MET* 3.7 29.8 - - + -
2112C PRO* 2.8 16.1 + - + +
2114C THR* 1.3 83.9 - - + +
2116C ARG* 1.3 57.2 + - - +
2118C PHE* 3.3 6.6 + - - +
2119C VAL* 3.0 40.7 + - + +
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Residues in contact with ARG2116 (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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2103C TYR* 4.1 8.1 - - + -
2110C ARG* 5.1 6.4 - - - +
2111C MET* 2.8 44.4 + - + +
2112C PRO 2.9 8.4 + - - +
2113C PRO* 4.0 27.5 - - + +
2115C VAL* 1.3 78.9 - - - +
2117C ALA* 1.3 61.1 + - - +
2120C ALA* 3.2 9.9 + - - +
2126C GLN* 3.0 44.7 + - - +
2128C GLU* 4.4 17.4 + - - -
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Residues in contact with ALA2117 (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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2113C PRO 2.6 24.3 + - - +
2114C THR* 3.8 4.9 - - - +
2116C ARG* 1.3 71.6 - - - +
2118C PHE* 1.3 66.1 + - - +
2119C VAL 3.2 0.2 + - - -
2120C ALA* 3.4 2.6 + - - +
2121C SER* 2.9 23.9 + - - -
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Residues in contact with PHE2118 (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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1930C GLN* 3.0 44.9 - - - -
2092C CYS* 3.9 26.5 - - + -
2095C THR* 3.9 12.3 - - - -
2114C THR 3.1 11.9 + - - +
2115C VAL* 3.6 8.1 - - - +
2117C ALA* 1.3 79.2 - - - +
2119C VAL* 1.3 68.3 + - - +
2121C SER* 2.3 32.0 + - - -
2122C ARG* 3.2 36.2 + - + +
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Residues in contact with VAL2119 (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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2091C ALA* 3.7 26.0 - - + +
2092C CYS* 4.3 6.1 - - - -
2095C THR* 4.0 12.2 - - + +
2101C LEU* 4.7 2.7 - - + -
2103C TYR* 4.5 2.0 - - - +
2115C VAL* 3.0 34.0 + - + +
2117C ALA 3.2 0.4 - - - -
2118C PHE* 1.3 77.8 - - - +
2120C ALA* 1.3 62.0 + - - +
2122C ARG* 3.2 10.4 + - - +
2123C GLY 3.3 0.2 + - - -
2124C THR* 3.3 36.9 + - + +
2126C GLN* 3.2 40.4 - - + +
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Residues in contact with ALA2120 (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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2116C ARG 3.2 10.3 + - - +
2117C ALA* 4.1 2.7 - - - +
2119C VAL* 1.3 77.6 - - - +
2121C SER* 1.3 64.3 + - - +
2123C GLY* 3.0 14.4 + - - -
2124C THR 4.1 9.6 - - - +
2126C GLN* 3.2 14.9 - - - +
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Residues in contact with SER2121 (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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2117C ALA 2.9 14.7 + - - -
2118C PHE* 2.3 33.4 + - - -
2120C ALA* 1.3 77.3 - - - +
2122C ARG* 1.3 75.0 + - - +
2123C GLY* 3.4 0.7 + - - -
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Residues in contact with ARG2122 (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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2095C THR* 3.8 29.0 + - - +
2096C GLN* 5.9 4.6 - - - +
2118C PHE* 3.2 38.7 + - + +
2119C VAL 3.2 2.7 + - - +
2121C SER* 1.3 90.4 + - - +
2123C GLY* 1.3 58.2 + - - +
2124C THR* 3.9 1.1 - - - -
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Residues in contact with GLY2123 (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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2120C ALA* 3.0 15.2 + - - -
2121C SER 3.2 1.3 - - - -
2122C ARG* 1.3 79.3 - - - +
2124C THR* 1.3 62.9 + - - +
2125C LYS* 3.2 25.2 + - - +
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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