Contacts of the strand formed by residues 100 - 105 (chain V) in PDB entry 2GLJ
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 LYS 100 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99V PHE* 1.3 78.1 - - - +
101V ILE* 1.3 62.3 + - - +
102V LEU* 5.1 2.9 - - - +
285V LYS* 4.4 27.8 - - + +
286V THR 3.3 5.7 + - - -
287V CYS* 3.1 22.5 - - + +
288V ILE 3.0 19.6 + - - +
337V GLU* 2.9 32.6 + - + +
395V ILE* 5.0 1.8 - - - +
462V PHE* 3.5 55.5 + - + +
463V LEU* 4.3 13.0 - - - +
465V ASN 3.3 28.5 + - - +
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Residues in contact with ILE 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99V PHE* 4.0 14.8 - - + -
100V LYS* 1.3 73.2 - - - +
102V LEU* 1.3 71.8 + - - +
288V ILE* 3.1 26.7 - - + +
290V ILE* 3.5 29.6 - - + -
309V PHE* 3.6 30.7 - - + -
333V LEU* 5.4 2.2 - - + -
336V SER* 4.7 1.8 - - - -
337V GLU 3.0 7.7 + - - +
338V MET* 3.3 21.5 - - + -
339V LEU 3.1 24.2 + - - -
423V LEU* 5.0 0.4 - - + -
428V MET* 3.3 27.6 - - + -
462V PHE* 4.0 1.7 - - - -
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Residues in contact with LEU 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100V LYS 5.1 2.9 - - - +
101V ILE* 1.3 84.5 - - - +
103V GLY* 1.3 58.5 + - - +
273V SER* 3.8 35.0 - - - +
276V ALA* 4.8 4.0 - - + -
277V MET* 4.8 5.2 - - + +
288V ILE 2.9 7.5 + - - +
289V THR* 3.3 16.7 - - - +
290V ILE 2.8 27.7 + - - +
339V LEU* 3.6 33.9 - - + +
459V TYR* 4.1 30.5 - - + +
462V PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101V ILE* 4.2 2.0 - - - +
102V LEU* 1.3 75.3 - - - +
104V ALA* 1.3 66.1 + - - +
273V SER* 5.6 1.8 - - - -
290V ILE* 3.5 13.2 - - - -
291V LEU* 5.2 0.2 - - - -
338V MET* 4.6 9.0 - - - +
339V LEU 3.9 8.5 + - - -
340V SER* 4.3 11.8 - - - +
341V SER* 3.1 28.9 + - - -
419V ILE* 5.5 2.5 - - - -
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Residues in contact with ALA 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103V GLY* 1.3 76.1 - - - +
105V HIS* 1.3 61.0 + - - +
266V ASP* 3.3 16.2 - - - +
269V CYS 4.4 0.4 - - - -
270V ALA* 3.8 32.5 - - + +
273V SER* 4.6 2.7 - - - +
290V ILE 3.1 5.1 + - - -
291V LEU* 3.1 31.7 - - + +
292V VAL* 3.2 3.7 + - - +
341V SER* 4.0 9.6 - - - +
419V ILE* 4.8 11.9 - - - +
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Residues in contact with HIS 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104V ALA* 1.3 70.0 - - - +
106V ILE* 1.3 60.2 + - - +
107V ASP* 2.8 44.0 + - - +
265V ASP* 3.3 17.9 - - - -
266V ASP* 2.4 70.5 + - + +
267V ARG 4.2 0.3 + - - -
270V ALA* 4.4 0.9 - - - +
292V VAL* 2.9 16.2 - - + +
295V GLU* 3.0 43.6 + - + -
296V GLU* 3.5 5.4 - - + -
341V SER 5.4 0.2 - - - -
342V ASP* 3.6 4.9 - - + -
419V ILE* 4.7 5.9 - - + +
6044V MN 2.4 25.0 + - - -
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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