Contacts of the strand formed by residues 2141 - 2144 (chain D) 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 VAL2141 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063D ILE* 4.0 25.8 - - + -
2067D LEU* 4.2 14.4 - - + -
2073D MET* 5.3 3.6 - - + -
2074D THR 3.2 4.5 + - - +
2075D ILE* 3.8 32.5 - - + +
2076D THR 2.9 25.6 + - - -
2139D THR* 3.0 6.1 - - - +
2140D ASP* 1.3 81.7 - - + +
2142D LEU* 1.3 60.0 + - - +
2143D TYR* 3.6 10.2 + - + +
2180D VAL* 3.5 7.2 - - + +
2182D MET* 3.6 32.5 - - + -
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Residues in contact with LEU2142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2076D THR* 3.8 13.0 - - + +
2078D VAL* 3.9 27.4 - - + -
2132D ILE* 4.7 8.5 - - + +
2136D LEU* 4.2 18.2 - - + -
2139D THR* 3.6 6.8 - - + +
2140D ASP 4.1 0.4 - - - -
2141D VAL* 1.3 69.3 - - - +
2143D TYR* 1.3 56.8 + - - +
2144D MET* 3.4 11.3 + - - -
2167D LEU* 3.6 43.5 - - + -
2172D MET* 4.4 0.4 - - - -
2179D MET* 3.6 27.1 - - + +
2180D VAL 2.8 9.3 + - - -
2181D VAL* 3.4 4.8 - - + +
2182D MET 2.9 26.6 + - - +
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Residues in contact with TYR2143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059D ASP* 2.7 35.9 + - - -
2063D ILE* 6.2 0.2 - - + -
2075D ILE* 4.3 10.5 - - + -
2076D THR 2.9 14.6 + - - +
2077D MET* 4.2 9.9 - - + -
2078D VAL 3.0 24.3 + - - +
2086D THR* 3.4 17.4 - - - -
2087D VAL* 3.3 33.9 - - + -
2090D LEU* 3.3 22.6 - - + +
2141D VAL* 3.6 4.8 + - + -
2142D LEU* 1.3 69.0 - - - +
2144D MET* 1.3 58.1 + - - +
2145D THR* 3.6 15.1 + - + +
2182D MET* 3.6 22.2 - - + -
2184D PRO* 3.4 23.0 - - + +
2206D GLN* 4.0 9.9 - - - -
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Residues in contact with MET2144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2078D VAL* 3.7 29.2 - - + +
2132D ILE* 4.1 15.3 - - + -
2142D LEU* 4.0 22.7 - - + +
2143D TYR* 1.3 71.8 - - - +
2145D THR* 1.3 60.8 + - - +
2165D PHE* 4.7 2.7 - - + +
2167D LEU* 3.9 13.0 - - + +
2181D VAL* 4.0 14.4 - - + -
2182D MET 2.8 13.0 + - - +
2183D HIS* 3.0 33.1 + - + -
2184D PRO* 3.5 5.0 - - - +
2190D GLU* 3.2 37.9 - - + +
2191D ILE* 3.8 25.8 - - + -
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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