Contacts of the strand formed by residues 100 - 105 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PHE* 1.3 79.1 - - - +
101E ILE* 1.3 61.6 + - - +
102E LEU* 4.1 2.8 + - - +
285E LYS* 4.5 20.2 - - + +
286E THR 3.3 5.7 + - - -
287E CYS* 3.1 21.7 - - + +
288E ILE 3.0 19.8 + - - +
337E GLU* 2.9 31.3 + - + +
395E ILE* 5.0 3.4 - - - +
462E PHE* 3.6 57.6 + - + +
463E LEU 4.2 5.6 - - - +
464E ASN* 4.1 11.2 + - - -
465E ASN* 3.9 32.7 + - - +
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Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PHE* 4.0 14.1 - - + -
100E LYS* 1.3 74.6 - - - +
102E LEU* 1.3 71.8 + - - +
288E ILE* 3.1 27.1 - - + +
290E ILE* 3.4 29.4 - - + -
309E PHE* 3.6 31.2 - - + -
333E LEU* 5.4 1.8 - - + -
336E SER* 4.7 1.8 - - - +
337E GLU 3.0 7.3 + - - +
338E MET* 3.3 21.3 - - + -
339E LEU 3.0 23.0 + - - -
423E LEU* 5.0 0.2 - - + -
428E MET* 3.3 27.8 - - + -
462E PHE* 4.0 2.4 - - - -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LYS 5.1 2.9 - - - +
101E ILE* 1.3 85.5 - - - +
103E GLY* 1.3 54.1 + - - +
273E SER* 3.8 39.0 - - - +
276E ALA* 4.7 3.8 - - + -
277E MET* 4.8 4.5 - - + +
288E ILE 2.9 7.0 + - - +
289E THR* 3.3 16.7 - - - +
290E ILE 2.7 32.9 + - - +
339E LEU* 3.6 34.5 - - + +
459E TYR* 4.1 28.0 - - + +
462E PHE* 4.0 12.3 - - + -
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Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ILE* 4.2 2.0 - - - +
102E LEU* 1.3 74.8 - - - +
104E ALA* 1.3 65.6 + - - +
273E SER* 5.6 1.6 - - - -
290E ILE* 3.5 13.2 - - - -
338E MET* 4.6 7.5 - - - +
339E LEU 3.8 10.5 + - - +
340E SER* 4.3 10.0 - - - +
341E SER* 3.0 29.8 + - - -
419E ILE* 5.5 2.9 - - - -
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E GLY* 1.3 76.6 - - - +
105E HIS* 1.3 60.5 + - - +
266E ASP* 3.3 15.3 - - - +
269E CYS 4.4 0.4 - - - -
270E ALA* 3.8 32.1 - - + +
273E SER* 4.6 2.7 - - - +
290E ILE 3.1 5.3 + - - -
291E LEU* 3.2 31.1 - - + +
292E VAL* 3.2 4.4 + - - +
341E SER* 4.0 10.3 - - - +
419E ILE* 4.8 11.1 - - - +
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Residues in contact with HIS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ALA* 1.3 70.1 - - - +
106E ILE* 1.3 60.1 + - - +
107E ASP* 2.8 43.0 + - - +
265E ASP* 3.2 11.8 + - - -
266E ASP* 2.4 68.5 + - + +
267E ARG 4.2 0.5 + - - -
270E ALA* 4.4 0.5 - - - +
292E VAL* 2.9 16.2 - - + +
295E GLU* 3.0 41.5 + - + -
296E GLU* 3.5 5.2 - - + -
341E SER 5.4 0.2 - - - -
342E ASP* 3.5 5.6 - - + -
419E ILE* 4.7 6.9 - - + +
6010E MN 2.3 34.1 + - - -
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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