Contacts of the strand formed by residues 100 - 105 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99N PHE* 1.3 78.2 - - - +
101N ILE* 1.3 62.6 + - - +
102N LEU* 5.1 3.1 - - - +
285N LYS* 4.4 27.1 - - + +
286N THR 3.3 5.1 + - - -
287N CYS* 3.1 21.9 - - + +
288N ILE 3.0 20.1 + - - +
337N GLU* 2.9 31.1 + - + +
395N ILE* 5.0 2.2 - - - +
462N PHE* 3.6 56.7 + - + +
463N LEU* 4.2 8.7 - - - +
464N ASN 3.8 8.7 + - - -
465N ASN* 3.0 25.6 + - - +
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Residues in contact with ILE 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N PHE* 4.0 15.0 - - + -
100N LYS* 1.3 76.3 - - - +
102N LEU* 1.3 71.3 + - - +
288N ILE* 3.1 27.4 - - + +
290N ILE* 3.4 28.7 - - + -
309N PHE* 3.6 31.4 - - + -
333N LEU* 5.4 2.2 - - + -
336N SER* 4.7 1.8 - - - +
337N GLU 2.9 7.1 + - - +
338N MET* 3.3 22.1 - - + -
339N LEU 3.1 23.1 + - - -
423N LEU* 5.0 0.2 - - + -
428N MET* 3.4 27.6 - - + -
462N PHE* 3.9 2.1 - - - -
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Residues in contact with LEU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100N LYS 5.1 2.7 - - - +
101N ILE* 1.3 84.2 - - - +
103N GLY* 1.3 58.6 + - - +
273N SER* 3.8 35.0 - - - +
276N ALA* 4.8 3.6 - - + -
277N MET* 4.8 5.4 - - + +
288N ILE 2.9 6.6 + - - +
289N THR* 3.3 16.8 - - - +
290N ILE 2.7 27.7 + - - +
339N LEU* 3.6 35.7 - - + +
459N TYR* 4.1 30.3 - - + +
462N PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N ILE* 4.2 1.6 - - - +
102N LEU* 1.3 75.6 - - - +
104N ALA* 1.3 66.6 + - - +
273N SER* 5.6 1.6 - - - -
290N ILE* 3.4 13.7 - - - -
338N MET* 4.6 8.4 - - - +
339N LEU 3.8 7.5 + - - -
340N SER* 4.3 12.8 - - - +
341N SER* 3.1 28.8 + - - -
419N ILE* 5.5 2.5 - - - -
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Residues in contact with ALA 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N GLY* 1.3 76.7 - - - +
105N HIS* 1.3 61.0 + - - +
266N ASP* 3.3 15.9 - - - +
269N CYS 4.5 0.7 - - - -
270N ALA* 3.8 32.3 - - + +
273N SER* 4.6 2.5 - - - +
290N ILE 3.1 5.1 + - - +
291N LEU* 3.1 14.4 - - + +
292N VAL* 3.1 21.8 + - - +
341N SER* 4.0 9.2 - - - +
419N ILE* 4.8 11.2 - - - +
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Residues in contact with HIS 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N ALA* 1.3 69.4 - - - +
106N ILE* 1.3 60.2 + - - +
107N ASP* 2.8 44.5 + - - +
265N ASP* 3.2 17.9 - - - -
266N ASP* 2.4 69.8 + - + +
267N ARG 4.2 0.3 + - - -
270N ALA* 4.4 0.7 - - - +
292N VAL* 2.9 15.9 - - + +
295N GLU* 3.0 40.9 + - + -
296N GLU* 3.5 4.9 - - + -
341N SER 5.4 0.2 - - - -
342N ASP* 3.6 4.5 - - + -
419N ILE* 4.7 6.3 - - + +
6028N MN 2.4 28.5 + - - -
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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