Contacts of the strand formed by residues 2099 - 2104 (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 VAL2099 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070C VAL* 3.9 25.8 - - + +
2072C GLY 5.2 0.7 - - - -
2073C MET 3.3 11.9 - - - +
2075C ILE* 3.4 24.5 - - + -
2094C LEU* 3.5 33.4 - - + +
2097C TYR* 3.4 7.2 + - + +
2098C ARG* 1.3 79.1 - - - +
2100C SER* 1.3 62.9 + - - +
2101C LEU* 4.2 8.1 - - + -
2124C THR* 3.5 28.9 - - + +
2125C LYS* 4.7 7.3 + - - -
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Residues in contact with SER2100 (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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2073C MET 3.1 3.4 + - - -
2074C THR* 3.1 32.0 + - - +
2075C ILE* 3.1 23.0 + - - +
2099C VAL* 1.3 76.5 - - - +
2101C LEU* 1.3 65.3 + - - +
2102C ARG* 5.3 1.3 - - - -
2124C THR* 4.5 0.7 - - - -
2125C LYS* 3.8 14.8 - - - +
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Residues in contact with LEU2101 (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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2075C ILE* 3.7 26.2 - - + +
2077C MET* 4.3 4.5 - - + -
2091C ALA* 3.4 44.9 - - + +
2094C LEU* 3.6 25.1 - - + -
2099C VAL* 4.2 4.3 - - + -
2100C SER* 1.3 75.3 - - - +
2102C ARG* 1.3 63.4 + - - +
2103C TYR* 3.7 27.2 + - + +
2119C VAL* 4.7 6.3 - - + -
2124C THR* 4.4 12.0 - - + +
2125C LYS 3.2 8.9 + - - +
2126C GLN* 3.4 9.0 - - + +
2127C GLU* 2.8 27.2 + - - +
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Residues in contact with ARG2102 (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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2074C THR* 3.7 20.9 - - + +
2075C ILE 3.1 5.7 + - - +
2076C THR* 3.1 29.2 - - + +
2077C MET* 2.7 32.4 + - - +
2100C SER* 5.3 1.1 - - - -
2101C LEU* 1.3 77.0 - - - +
2103C TYR* 1.3 59.0 + - - +
2127C GLU* 3.3 14.2 + - + +
2129C PHE* 3.3 42.8 - - + -
2134C GLU 4.6 2.6 + - - -
2135C ALA* 2.6 38.2 + - - +
2137C PRO* 5.2 0.2 - - - +
2138C ASP* 3.5 41.6 + - - +
2139C THR* 4.1 1.8 + - - +
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Residues in contact with TYR2103 (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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2077C MET* 3.5 24.2 - - + -
2081C LEU* 3.7 23.1 - - + -
2091C ALA* 4.0 4.3 - - - +
2101C LEU* 3.7 21.7 - - + +
2102C ARG* 1.3 77.3 - - - +
2104C VAL* 1.3 61.1 + - - +
2105C ALA* 4.2 1.5 + - + -
2110C ARG* 6.3 2.0 - - - -
2111C MET* 3.7 42.8 - - + +
2116C ARG* 4.1 6.1 - - + -
2119C VAL* 4.4 1.4 - - - +
2126C GLN* 2.7 48.7 + - + +
2127C GLU 2.8 18.4 + - - +
2128C GLU* 3.5 23.0 - - + +
2129C PHE 2.9 26.0 + - - +
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Residues in contact with VAL2104 (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 THR* 3.6 24.5 - - + -
2077C MET 2.7 12.0 + - - +
2078C VAL* 3.1 20.3 - - + +
2079C GLY 3.0 23.7 + - - -
2081C LEU* 4.0 0.7 - - - +
2103C TYR* 1.3 77.5 - - - +
2105C ALA* 1.3 64.1 + - - +
2129C PHE* 3.7 10.8 - - + +
2131C SER* 3.6 43.5 - - - +
2132C ILE* 4.3 2.0 - - - +
2135C ALA* 4.0 6.3 - - + -
2165C PHE* 3.8 19.3 - - + -
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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