Contacts of the strand formed by residues 96 - 100 (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 LEU 96 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G GLY* 1.3 78.5 - - - +
97G LYS* 1.3 62.8 + - - +
108G LEU* 5.1 5.6 - - + -
109G PHE 5.0 5.6 - - - +
111G PRO* 3.9 31.6 - - + +
114G ASN* 3.7 29.6 - - + +
115G MET* 5.0 7.6 - - + -
136G LEU* 5.4 1.1 - - + -
139G ILE* 5.3 6.3 - - + -
159G TYR* 3.5 4.0 - - - -
160G ILE* 2.6 78.6 + - + +
162G PRO* 3.8 17.9 - - + -
331G THR* 4.0 7.4 - - - -
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G LEU* 1.3 83.1 - - - +
98G ALA* 1.3 59.1 + - - +
99G PHE* 3.5 39.4 - - + -
108G LEU* 3.7 18.2 - - - +
109G PHE* 3.9 4.8 + - - +
157G SER* 3.3 24.0 + - - +
158G LEU 3.2 8.1 - - - +
159G TYR* 4.1 12.8 - - + -
160G ILE* 4.0 5.6 - - - +
188G VAL* 3.9 20.9 - - - +
189G GLY 4.9 3.2 + - - -
331G THR* 3.1 39.6 + - + +
332G ALA* 3.3 19.6 + - - +
334G VAL* 5.8 3.2 - - - +
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Residues in contact with ALA 98 (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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97G LYS* 1.3 73.7 - - - +
99G PHE* 1.3 62.1 + - - +
106G ILE* 4.0 17.3 - - + -
107G ARG 3.3 4.7 - - - -
108G LEU* 3.8 17.9 - - + -
143G VAL* 4.1 16.4 - - + -
150G VAL* 3.9 4.8 - - + +
157G SER* 3.3 6.9 - - - -
158G LEU* 2.8 43.2 + - + +
160G ILE* 4.0 4.8 - - + +
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Residues in contact with PHE 99 (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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97G LYS* 3.5 40.4 - - + -
98G ALA* 1.3 74.3 - - - +
100G ARG* 1.3 62.4 + - - +
101G GLY* 3.2 3.6 + - - -
105G LYS 3.5 0.2 - - - +
106G ILE* 3.4 1.0 - - - -
107G ARG* 2.9 46.5 + - + +
109G PHE* 4.0 14.4 - - + -
150G VAL* 4.0 3.1 - - - -
157G SER* 3.6 25.4 - - - +
371G GLN* 3.5 65.9 - - + +
372G TYR* 3.6 32.5 - + + -
380G THR* 6.3 0.2 - - + -
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Residues in contact with ARG 100 (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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99G PHE* 1.3 68.6 - - - +
101G GLY* 1.3 69.9 + - - +
104G ASN* 3.2 39.6 + - - +
105G LYS 3.9 3.4 - - - -
106G ILE* 3.6 25.8 - - - +
147G GLN* 3.1 23.6 + - - -
148G GLU* 3.7 12.3 + - - +
150G VAL* 2.6 45.5 + - + +
151G PRO 3.4 22.4 + - - +
152G TYR* 3.2 50.3 + - + +
153G SER 4.7 4.5 - - - +
154G THR* 4.7 3.8 - - - +
156G ALA 5.3 1.6 + - - -
372G TYR* 3.3 20.5 - - - -
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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