Contacts of the strand formed by residues 100 - 105 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99P PHE* 1.3 79.2 - - - +
101P ILE* 1.3 60.8 + - - +
102P LEU* 5.1 2.6 - - - +
285P LYS* 4.5 27.8 - - + +
286P THR 3.3 5.7 + - - -
287P CYS* 3.1 22.1 - - + +
288P ILE 2.9 20.8 + - - +
337P GLU* 2.9 31.4 + - + +
395P ILE* 5.0 3.0 - - - +
462P PHE* 3.6 57.7 + - + +
463P LEU 4.3 13.7 - - - +
464P ASN* 4.8 1.7 + - - +
465P ASN* 4.5 16.4 - - - +
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Residues in contact with ILE 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P PHE* 4.0 14.6 - - + -
100P LYS* 1.3 74.0 - - - +
102P LEU* 1.3 74.6 + - - +
288P ILE* 3.1 26.7 - - + +
290P ILE* 3.4 29.8 - - + -
309P PHE* 3.6 30.3 - - + -
333P LEU* 5.4 2.0 - - + -
336P SER* 4.7 1.8 - - - -
337P GLU 3.0 7.1 + - - +
338P MET* 3.3 18.2 - - + -
339P LEU 3.1 23.5 + - - -
423P LEU* 5.0 0.2 - - + -
428P MET* 3.3 28.0 - - + -
462P PHE* 3.9 2.1 - - - -
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Residues in contact with LEU 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P LYS 5.1 2.9 - - - +
101P ILE* 1.3 85.3 - - - +
103P GLY* 1.3 54.0 + - - +
273P SER* 3.8 37.5 - - - +
276P ALA* 4.8 3.8 - - + -
277P MET* 4.8 5.8 - - + +
288P ILE 2.8 8.3 + - - +
289P THR* 3.3 15.9 - - - +
290P ILE 2.7 33.3 + - - +
339P LEU* 3.6 34.5 - - + +
459P TYR* 4.1 27.4 - - + +
462P PHE* 4.0 12.6 - - + -
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Residues in contact with GLY 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P ILE* 4.2 1.8 - - - +
102P LEU* 1.3 75.0 - - - +
104P ALA* 1.3 65.5 + - - +
273P SER* 5.6 1.6 - - - -
290P ILE* 3.5 14.1 - - - -
291P LEU* 5.2 0.2 - - - -
338P MET* 4.6 7.5 - - - +
339P LEU 3.8 7.9 + - - +
340P SER* 4.3 12.4 - - - +
341P SER* 3.0 29.6 + - - -
419P ILE* 5.5 2.7 - - - -
423P LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P GLY* 1.3 77.9 - - - +
105P HIS* 1.3 60.2 + - - +
266P ASP* 3.3 15.9 - - - +
269P CYS 4.5 0.7 - - - -
270P ALA* 3.7 32.3 - - + +
273P SER* 4.6 1.8 - - - +
290P ILE* 3.2 5.3 + - - +
291P LEU* 3.1 31.2 - - + +
292P VAL* 3.2 4.8 + - - +
340P SER* 6.0 0.2 - - - -
341P SER* 3.9 9.6 - - - +
419P ILE* 4.8 11.7 - - - +
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Residues in contact with HIS 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ALA* 1.3 70.1 - - - +
106P ILE* 1.3 59.8 + - - +
107P ASP* 2.7 45.5 + - - +
265P ASP* 3.2 12.6 - - - -
266P ASP* 2.4 72.4 + - + +
267P ARG 4.2 0.3 + - - -
270P ALA* 4.4 0.7 - - - +
292P VAL* 2.9 16.8 - - + +
295P GLU* 3.1 37.2 + - + -
296P GLU* 3.5 4.9 - - + -
341P SER 5.4 0.2 - - - -
342P ASP* 3.6 5.2 - - + -
419P ILE* 4.7 5.7 - - + +
6032P MN 2.1 37.3 + - - -
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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