Contacts of the strand formed by residues 100 - 105 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G PHE* 1.3 76.9 - - - +
101G ILE* 1.3 61.5 + - - +
102G LEU* 4.1 3.3 + - - +
285G LYS* 4.5 26.2 - - + +
286G THR 3.3 6.4 + - - +
287G CYS* 3.1 22.2 - - + +
288G ILE 3.0 20.8 + - - +
337G GLU* 2.9 29.9 + - + +
395G ILE* 5.0 0.8 - - - +
462G PHE* 3.6 54.7 + - + +
463G LEU 4.3 10.8 - - - +
465G ASN* 3.0 35.8 + - - +
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Residues in contact with ILE 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G PHE* 4.0 14.6 - - + -
100G LYS* 1.3 75.0 - - - +
102G LEU* 1.3 72.2 + - - +
288G ILE* 3.1 26.7 - - + +
290G ILE* 3.5 28.9 - - + -
309G PHE* 3.6 31.4 - - + -
333G LEU* 5.4 2.5 - - + -
336G SER* 4.7 2.0 - - - -
337G GLU 3.0 7.3 + - - +
338G MET* 3.3 22.7 - - + -
339G LEU 3.0 23.2 + - - -
428G MET* 3.4 27.1 - - + -
462G PHE* 4.0 2.1 - - - -
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Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G LYS 5.1 2.5 - - - +
101G ILE* 1.3 84.8 - - - +
103G GLY* 1.3 59.4 + - - +
273G SER* 3.8 38.8 - - - +
276G ALA* 4.8 3.4 - - + -
277G MET* 4.8 5.6 - - + +
288G ILE 2.9 6.8 + - - +
289G THR* 3.3 16.8 - - - +
290G ILE* 2.7 28.4 + - - +
339G LEU* 3.6 34.3 - - + +
459G TYR* 4.1 28.3 - - + -
462G PHE* 4.0 11.9 - - + -
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Residues in contact with GLY 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G ILE* 4.2 2.0 - - - +
102G LEU* 1.3 75.0 - - - +
104G ALA* 1.3 65.7 + - - +
273G SER* 5.6 1.6 - - - -
290G ILE* 3.5 12.6 - - - -
291G LEU* 5.2 0.2 - - - -
338G MET* 4.6 8.2 - - - +
339G LEU 3.9 7.1 + - - -
340G SER* 4.3 12.4 - - - +
341G SER* 3.0 29.4 + - - -
419G ILE* 5.5 2.0 - - - -
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G GLY* 1.3 76.8 - - - +
105G HIS* 1.3 60.4 + - - +
266G ASP* 3.3 16.4 - - - +
269G CYS 4.4 0.7 - - - -
270G ALA* 3.8 32.5 - - + +
273G SER* 4.6 2.0 - - - +
290G ILE 3.1 4.5 + - - -
291G LEU* 3.1 32.2 - - + +
292G VAL* 3.2 4.2 + - - +
341G SER* 3.9 10.1 - - - +
419G ILE* 4.8 11.9 - - - +
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Residues in contact with HIS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ALA* 1.3 70.7 - - - +
106G ILE* 1.3 59.4 + - - +
107G ASP* 2.7 43.6 + - - +
265G ASP* 3.2 12.3 + - - -
266G ASP* 2.4 67.6 + - + +
267G ARG 4.2 0.3 + - - -
270G ALA* 4.3 0.9 - - - +
292G VAL* 2.9 16.2 - - + +
295G GLU* 3.0 41.6 + - + -
296G GLU* 3.5 5.6 - - + -
341G SER 5.4 0.4 - - - -
342G ASP* 3.6 4.5 - - + -
419G ILE* 4.7 5.9 - - + +
6014G MN 2.1 36.2 + - - -
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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