Contacts of the strand formed by residues 100 - 105 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q PHE* 1.3 77.7 - - - +
101Q ILE* 1.3 61.9 + - - +
102Q LEU* 5.1 3.2 - - - +
285Q LYS* 4.5 27.8 - - + +
286Q THR 3.3 5.7 + - - -
287Q CYS* 3.1 23.7 - - + +
288Q ILE 2.9 20.5 + - - +
337Q GLU* 2.9 31.0 + - + +
395Q ILE* 5.0 4.8 - - - +
462Q PHE* 3.5 58.3 + - + +
463Q LEU* 4.3 13.9 - - - +
464Q ASN 4.6 9.8 + - - -
465Q ASN* 4.8 10.4 - - - +
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Residues in contact with ILE 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q PHE* 4.0 14.6 - - + -
100Q LYS* 1.3 75.0 - - - +
102Q LEU* 1.3 73.7 + - - +
288Q ILE* 3.2 27.1 - - + +
290Q ILE* 3.5 29.4 - - + -
309Q PHE* 3.6 30.7 - - + -
333Q LEU* 5.4 2.5 - - + -
336Q SER* 4.7 1.6 - - - -
337Q GLU 2.9 9.5 + - - +
338Q MET* 3.3 19.4 - - + -
339Q LEU 3.0 23.8 + - - -
423Q LEU* 5.0 0.4 - - + -
428Q MET* 3.3 26.9 - - + -
462Q PHE* 4.0 2.1 - - - -
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Residues in contact with LEU 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q LYS 5.1 2.7 - - - +
101Q ILE* 1.3 85.0 - - - +
103Q GLY* 1.3 58.5 + - - +
273Q SER* 3.8 38.4 - - - +
276Q ALA* 4.8 3.8 - - + -
277Q MET* 4.8 4.9 - - + +
288Q ILE 2.9 6.4 + - - +
289Q THR* 3.3 17.5 - - - +
290Q ILE 2.8 27.5 + - - +
339Q LEU* 3.6 33.2 - - + +
459Q TYR* 4.1 27.1 - - + +
462Q PHE* 4.1 12.8 - - + -
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Residues in contact with GLY 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ILE* 4.2 1.6 - - - +
102Q LEU* 1.3 75.6 - - - +
104Q ALA* 1.3 65.3 + - - +
273Q SER* 5.6 2.2 - - - -
290Q ILE* 3.5 13.7 - - - -
291Q LEU* 5.2 0.2 - - - -
338Q MET* 4.6 8.1 - - - +
339Q LEU 3.8 8.3 + - - +
340Q SER* 4.3 11.1 - - - +
341Q SER* 3.0 29.4 + - - -
419Q ILE* 5.5 2.7 - - - -
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Residues in contact with ALA 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q GLY* 1.3 77.4 - - - +
105Q HIS* 1.3 59.8 + - - +
266Q ASP* 3.3 16.2 - - - +
269Q CYS 4.5 0.4 - - - -
270Q ALA* 3.8 32.1 - - + +
273Q SER* 4.6 2.5 - - - +
290Q ILE* 3.1 5.7 + - - +
291Q LEU* 3.2 32.0 - - + +
292Q VAL* 3.2 4.4 + - - +
341Q SER* 4.0 9.4 - - - +
419Q ILE* 4.8 11.7 - - - +
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Residues in contact with HIS 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q ALA* 1.3 69.3 - - - +
106Q ILE* 1.3 60.8 + - - +
107Q ASP* 2.8 44.3 + - - +
265Q ASP* 3.1 18.9 + - - -
266Q ASP* 2.4 68.1 + - + +
267Q ARG 4.2 0.3 + - - -
270Q ALA* 4.4 0.7 - - - +
292Q VAL* 2.9 16.4 - - + +
295Q GLU* 3.0 43.4 + - + -
296Q GLU* 3.5 5.2 - - + -
341Q SER 5.4 0.2 - - - -
342Q ASP* 3.6 4.3 - - + -
419Q ILE* 4.7 6.5 - - + +
6034Q MN 2.4 27.1 + - - -
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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