Contacts of the strand formed by residues 100 - 105 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F PHE* 1.3 79.1 - - - +
101F ILE* 1.3 61.6 + - - +
102F LEU* 5.1 2.6 - - - +
285F LYS* 4.5 28.7 - - + +
286F THR 3.3 5.7 + - - -
287F CYS* 3.1 21.9 - - + +
288F ILE 3.0 20.9 + - - +
337F GLU* 2.9 30.9 + - + +
395F ILE* 5.0 4.2 - - - +
462F PHE* 3.6 56.2 + - + +
463F LEU* 4.2 13.7 - - - +
464F ASN 4.3 7.5 + - - -
465F ASN* 4.2 13.9 + - - -
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Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F PHE* 4.0 14.8 - - + -
100F LYS* 1.3 73.8 - - - +
102F LEU* 1.3 72.5 + - - +
288F ILE* 3.1 26.7 - - + +
290F ILE* 3.5 29.2 - - + -
309F PHE* 3.6 30.5 - - + -
333F LEU* 5.4 2.0 - - + -
336F SER* 4.7 2.2 - - - +
337F GLU 3.0 6.9 + - - +
338F MET* 3.3 21.3 - - + -
339F LEU 3.0 23.9 + - - -
423F LEU* 5.0 0.4 - - + -
428F MET* 3.3 26.7 - - + -
462F PHE* 3.9 1.9 - - - -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LYS 5.1 2.9 - - - +
101F ILE* 1.3 83.5 - - - +
103F GLY* 1.3 58.4 + - - +
273F SER* 3.9 35.7 - - - +
276F ALA* 4.8 4.0 - - + -
277F MET* 4.8 5.6 - - + -
288F ILE 2.9 6.8 + - - +
289F THR* 3.3 16.3 - - - +
290F ILE 2.7 28.1 + - - +
339F LEU* 3.6 30.3 - - + +
459F TYR* 4.1 30.1 - - + +
462F PHE* 4.0 15.9 - - + -
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ILE* 4.2 1.6 - - - +
102F LEU* 1.3 76.7 - - - +
104F ALA* 1.3 66.0 + - - +
273F SER* 5.6 1.9 + - - -
290F ILE* 3.4 14.4 - - - -
291F LEU* 5.2 0.2 - - - -
338F MET* 4.6 7.2 - - - +
339F LEU 3.8 9.5 + - - -
340F SER* 4.3 9.6 - - - +
341F SER* 3.1 29.1 + - - -
419F ILE* 5.5 2.5 - - - -
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLY* 1.3 76.2 - - - +
105F HIS* 1.3 61.1 + - - +
266F ASP* 3.3 16.8 - - - +
269F CYS 4.5 0.2 - - - -
270F ALA* 3.8 31.4 - - + +
273F SER* 4.6 2.5 - - - +
290F ILE 3.1 5.3 + - - +
291F LEU* 3.1 31.3 - - + +
292F VAL* 3.1 4.8 + - - +
341F SER* 4.0 9.4 - - - +
419F ILE* 4.8 11.2 - - - +
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ALA* 1.3 70.5 - - - +
106F ILE* 1.3 59.9 + - - +
107F ASP* 2.8 44.3 + - - +
265F ASP* 3.1 19.2 + - - -
266F ASP* 2.4 70.1 + - + +
267F ARG 4.2 0.5 + - - -
270F ALA* 4.4 0.5 - - - +
292F VAL* 2.9 15.3 - - + +
295F GLU* 3.0 42.9 + - + -
296F GLU* 3.5 4.9 - - + -
341F SER 5.4 0.2 - - - -
342F ASP* 3.6 6.3 - - + -
419F ILE* 4.7 6.1 - - + +
6012F MN 2.5 23.8 + - - -
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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