Contacts of the strand formed by residues 106 - 109 (chain G) in PDB entry 2ABJ
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 ILE 106 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G ALA* 4.0 25.6 - - + -
99G PHE 3.4 5.8 - - - +
100G ARG* 3.6 35.4 - - - +
104G ASN 3.7 2.0 + - - +
105G LYS* 1.3 74.9 - - - +
107G ARG* 1.3 64.4 + - - +
108G LEU* 5.6 0.9 - - + -
143G VAL* 4.7 1.1 - - + -
147G GLN* 3.7 38.6 - - + +
150G VAL* 4.1 20.9 - - + -
382G VAL* 3.3 8.2 - - - +
383G LEU* 3.0 53.9 + - + +
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Residues in contact with ARG 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G ALA* 3.3 5.4 - - - -
99G PHE* 2.9 41.5 + - - +
101G GLY* 3.6 13.5 - - - -
103G ASP* 2.6 41.8 + - - -
105G LYS* 3.8 11.8 + - - +
106G ILE* 1.3 77.2 - - - +
108G LEU* 1.3 67.5 + - - +
371G GLN 4.0 14.1 + - - +
373G GLY* 3.3 37.2 + - - +
380G THR* 3.6 27.1 - - + -
381G ILE 3.3 15.3 - - - +
382G VAL* 3.8 26.9 - - + +
383G LEU 4.8 0.2 - - - +
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G LEU* 5.1 3.6 - - + -
97G LYS 3.7 15.9 - - - +
98G ALA* 3.8 20.2 - - + -
99G PHE* 5.2 0.2 - - - -
106G ILE* 5.6 1.3 - - + -
107G ARG* 1.3 75.5 - - - +
109G PHE* 1.3 61.6 + - - +
110G GLN 4.1 0.2 - - - -
111G PRO* 3.7 30.1 - - + -
136G LEU* 4.9 2.7 - - + -
139G ILE* 5.7 2.7 - - + -
140G GLN* 3.5 40.4 - - + +
143G VAL* 5.0 8.7 - - + -
160G ILE* 3.8 16.4 - - + -
379G TRP 3.9 0.2 - - - +
380G THR* 3.1 9.8 - - - -
381G ILE* 2.8 38.0 + - + +
383G LEU* 4.7 8.1 - - + -
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Residues in contact with PHE 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G LEU* 5.0 5.8 - - - +
97G LYS 3.9 7.8 + - - +
99G PHE* 4.0 20.2 - - + -
108G LEU* 1.3 74.5 - - - +
110G GLN* 1.3 78.4 + - + +
111G PRO* 3.1 3.8 - - - +
114G ASN* 4.2 6.8 + - - -
287G VAL* 4.4 11.5 - - + +
288G THR* 5.7 3.1 - - + -
291G CYS* 3.6 32.5 - - - -
367G LEU* 3.9 15.9 - - + -
370G ILE* 3.9 13.5 - - + -
371G GLN* 3.6 33.0 - - + -
379G TRP* 3.5 28.5 - + + -
380G THR* 3.9 14.8 - - + -
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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