Contacts of the strand formed by residues 2214 - 2217 (chain C) in PDB entry 1G24
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 GLU2214 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2079C TYR* 4.1 4.3 - - - -
2080C THR* 4.8 1.9 - - - +
2174C SER* 2.7 31.7 + - - -
2175C THR 3.1 15.7 - - - +
2202C TYR* 3.5 5.5 - - - -
2203C ILE* 3.1 54.6 + - + +
2204C ASP* 3.7 4.4 + - - +
2209C PHE 4.9 0.2 - - - +
2210C ALA* 3.5 9.3 - - + -
2211C GLY* 2.7 46.6 + - - +
2212C GLN 3.1 1.7 - - - -
2213C LEU* 1.3 76.7 - - - +
2215C MET* 1.3 66.6 + - - +
2216C LEU* 4.0 3.6 - - - +
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Residues in contact with MET2215 (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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2058C TRP* 4.1 15.0 - - + -
2062C GLN* 6.3 0.2 - - + -
2066C TYR* 5.2 2.0 - - - +
2120C THR* 4.8 3.6 - - - -
2124C ILE* 3.9 25.6 - - + -
2126C LEU* 3.9 11.4 - - + -
2173C ILE 3.8 0.7 - - - +
2175C THR* 2.8 48.2 + - - +
2177C LEU* 3.4 29.8 - - + +
2200C ALA* 4.0 26.7 - - + +
2201C GLY 3.2 4.9 - - - +
2202C TYR* 3.5 37.0 - - + +
2213C LEU 3.3 1.3 + - - +
2214C GLU* 1.3 74.1 - - - +
2216C LEU* 1.3 63.6 + - - +
2217C LEU* 3.9 1.0 + - - +
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Residues in contact with LEU2216 (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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2076C ILE* 5.4 4.5 - - + -
2079C TYR* 3.6 46.4 - - + +
2111C LEU* 5.0 11.7 - - + -
2115C PHE* 3.2 22.9 - - + -
2118C MET* 6.1 1.1 - - + -
2172C TYR* 4.0 16.4 - - + -
2173C ILE 3.7 10.1 - - - +
2174C SER* 3.7 13.7 - - - +
2200C ALA* 3.4 4.0 - - - -
2201C GLY 2.7 36.6 + - - +
2203C ILE* 4.1 23.1 - - + -
2214C GLU* 4.0 3.3 - - - +
2215C MET* 1.3 74.2 - - - +
2217C LEU* 1.3 66.4 + - - +
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Residues in contact with LEU2217 (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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2115C PHE* 3.7 3.1 - - - -
2126C LEU* 3.9 21.5 - - + -
2172C TYR* 3.7 9.7 - - - +
2173C ILE* 2.9 43.0 + - + +
2175C THR* 4.1 20.2 - - + -
2192C PHE* 4.9 2.7 - - + -
2194C VAL* 4.7 10.8 - - + -
2199C LYS 3.6 19.1 - - - +
2200C ALA* 3.6 18.2 - - + -
2215C MET 4.6 0.7 - - - +
2216C LEU* 1.3 76.4 - - - +
2218C PRO* 1.3 74.2 - - + +
2221C SER* 5.2 2.0 - - - +
2243C MET* 3.7 33.4 - - + -
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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