Contacts of the strand formed by residues 100 - 105 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99W PHE* 1.3 77.9 - - - +
101W ILE* 1.3 62.5 + - - +
102W LEU* 4.1 3.1 + - - +
285W LYS* 4.4 28.0 - - + +
286W THR 3.3 5.3 + - - -
287W CYS* 3.1 22.6 - - + +
288W ILE 3.0 20.1 + - - +
337W GLU* 3.0 31.6 + - + +
395W ILE* 5.0 8.7 - - - +
462W PHE* 3.6 58.3 + - + +
463W LEU* 4.3 15.4 - - - +
464W ASN* 5.3 5.3 - - - +
465W ASN 5.1 4.6 + - - +
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Residues in contact with ILE 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99W PHE* 4.0 14.4 - - + -
100W LYS* 1.3 74.2 - - - +
102W LEU* 1.3 72.4 + - - +
288W ILE* 3.1 27.4 - - + +
290W ILE* 3.5 28.7 - - + -
309W PHE* 3.6 30.3 - - + -
333W LEU* 5.4 1.8 - - + -
336W SER* 4.7 2.2 - - - +
337W GLU 3.0 7.3 + - - +
338W MET* 3.4 22.0 - - + -
339W LEU 3.1 23.4 + - - -
423W LEU* 5.0 0.4 - - + -
428W MET* 3.3 26.9 - - + -
462W PHE* 4.0 2.1 - - - -
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Residues in contact with LEU 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100W LYS 5.1 3.1 - - - +
101W ILE* 1.3 85.0 - - - +
103W GLY* 1.3 54.5 + - - +
273W SER* 3.9 35.2 - - - +
276W ALA* 4.8 3.6 - - + -
277W MET* 4.8 5.8 - - + +
288W ILE 2.8 7.5 + - - +
289W THR* 3.3 16.7 - - - +
290W ILE 2.7 33.3 + - - +
339W LEU* 3.6 31.0 - - + +
459W TYR* 4.1 30.3 - - + +
462W PHE* 4.0 15.9 - - + -
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Residues in contact with GLY 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101W ILE* 4.2 1.6 - - - +
102W LEU* 1.3 74.2 - - - +
104W ALA* 1.3 66.0 + - - +
273W SER* 5.6 2.0 + - - -
290W ILE* 3.4 14.6 - - - -
291W LEU* 5.2 0.2 - - - -
338W MET* 4.6 7.7 - - - +
339W LEU 3.9 8.7 + - - +
340W SER* 4.3 11.5 - - - +
341W SER* 3.1 28.1 + - - -
419W ILE* 5.5 2.5 - - - -
423W LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103W GLY* 1.3 77.0 - - - +
105W HIS* 1.3 59.8 + - - +
266W ASP* 3.3 16.2 - - - +
269W CYS 4.5 0.4 - - - -
270W ALA* 3.8 32.5 - - + +
273W SER* 4.6 2.2 - - - +
290W ILE 3.1 5.5 + - - +
291W LEU* 3.1 32.3 - - + +
292W VAL* 3.2 4.2 + - - +
341W SER* 4.0 9.4 - - - +
419W ILE* 4.8 11.9 - - - +
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Residues in contact with HIS 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W ALA* 1.3 70.5 - - - +
106W ILE* 1.3 60.3 + - - +
107W ASP* 2.8 42.8 + - - +
265W ASP* 3.2 19.1 + - - -
266W ASP* 2.4 69.5 + - + +
267W ARG 4.2 0.3 + - - -
270W ALA* 4.4 1.0 - - - +
292W VAL* 2.9 15.9 - - + +
295W GLU* 3.0 43.8 + - + -
296W GLU* 3.5 4.9 - - + -
341W SER 5.4 0.2 - - - -
342W ASP* 3.6 6.5 - - + -
419W ILE* 4.7 6.5 - - + +
6046W MN 2.7 23.2 + - - -
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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