Contacts of the strand formed by residues 100 - 105 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99H PHE* 1.3 78.5 - - - +
101H ILE* 1.3 62.8 + - - +
102H LEU* 5.1 2.8 - - - +
285H LYS* 4.4 28.0 - - + +
286H THR 3.3 5.8 + - - +
287H CYS* 3.1 21.7 - - + +
288H ILE 3.0 20.2 + - - +
337H GLU* 2.9 31.2 + - + +
395H ILE* 5.0 2.8 - - - +
462H PHE* 3.5 56.1 + - + +
463H LEU* 4.3 11.0 - - - +
464H ASN 5.2 0.2 - - - -
465H ASN* 2.8 29.9 + - - -
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Residues in contact with ILE 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H PHE* 3.9 15.0 - - + -
100H LYS* 1.3 75.2 - - - +
102H LEU* 1.3 73.8 + - - +
288H ILE* 3.2 27.6 - - + +
290H ILE* 3.5 29.2 - - + -
309H PHE* 3.6 31.4 - - + -
333H LEU* 5.4 1.8 - - + -
336H SER* 4.7 2.5 - - - +
337H GLU 2.9 7.9 + - - +
338H MET* 3.4 19.2 - - + -
339H LEU 3.1 23.4 + - - -
423H LEU* 5.0 0.2 - - + -
428H MET* 3.4 26.9 - - + -
462H PHE* 4.0 2.3 - - - -
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H LYS 5.1 2.5 - - - +
101H ILE* 1.3 83.2 - - - +
103H GLY* 1.3 60.2 + - - +
273H SER* 3.8 37.5 - - - +
276H ALA* 4.8 3.6 - - + -
277H MET* 4.8 5.6 - - + +
288H ILE 2.9 7.3 + - - +
289H THR* 3.3 17.1 - - - +
290H ILE 2.8 27.5 + - - +
339H LEU* 3.6 29.8 - - + +
459H TYR* 4.1 28.0 - - + +
462H PHE* 4.0 16.4 - - + -
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Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ILE* 4.2 2.0 - - - +
102H LEU* 1.3 74.9 - - - +
104H ALA* 1.3 66.1 + - - +
273H SER* 5.5 2.2 + - - -
290H ILE* 3.5 12.6 - - - -
291H LEU* 5.2 0.2 - - - -
338H MET* 4.6 8.4 - - - +
339H LEU 3.8 8.3 + - - +
340H SER* 4.3 11.3 - - - +
341H SER* 3.1 28.5 + - - -
419H ILE* 5.5 2.2 - - - -
423H LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLY* 1.3 76.3 - - - +
105H HIS* 1.3 60.0 + - - +
266H ASP* 3.3 15.7 - - - +
269H CYS 4.5 0.4 - - - -
270H ALA* 3.8 32.1 - - + +
273H SER* 4.6 3.1 - - - +
290H ILE* 3.1 5.3 + - - +
291H LEU* 3.1 32.0 - - + +
292H VAL* 3.2 4.6 + - - +
340H SER* 6.0 0.2 - - - -
341H SER* 4.0 9.0 - - - +
419H ILE* 4.8 11.5 - - - +
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Residues in contact with HIS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ALA* 1.3 69.3 - - - +
106H ILE* 1.3 59.5 + - - +
107H ASP* 2.8 43.7 + - - +
265H ASP* 3.2 17.3 - - - -
266H ASP* 2.4 70.0 + - + +
267H ARG 4.3 0.5 + - - -
270H ALA* 4.4 0.7 - - - +
292H VAL* 2.9 16.8 - - + +
295H GLU* 3.0 43.6 + - + -
296H GLU* 3.6 4.9 - - + -
342H ASP* 3.6 6.7 - - + -
419H ILE* 4.7 6.3 - - + +
6016H MN 2.7 23.4 + - - -
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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