Contacts of the strand formed by residues 291 - 296 (chain A) in PDB entry 1Q6D
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE 3.2 6.2 + - - +
176A ASP* 3.2 10.6 - - + +
177A ILE 2.8 26.0 + - - -
290A VAL* 1.3 79.5 - - - +
292A LEU* 1.3 65.4 + - - +
336A HIS 5.3 3.6 - - - +
338A ILE* 4.1 16.4 - - + -
376A ARG* 3.0 44.8 - - - +
414A PHE* 3.8 29.8 - - + -
457A ALA 4.7 9.7 + - - -
458A ILE* 4.2 30.3 - - + +
459A THR* 4.9 8.7 + - - +
461A LEU* 5.3 2.0 - - - -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 3.5 18.8 - - + +
179A VAL* 5.5 5.6 - - + -
278A LEU* 4.4 7.6 - - + +
281A ALA* 4.1 13.5 - - + -
282A ASN* 3.8 38.4 - - + +
285A PHE* 4.5 12.3 - - + -
290A VAL* 4.7 3.6 - - + -
291A LYS* 1.3 82.5 - - - +
293A ALA* 1.3 63.4 + - - +
335A HIS* 4.7 14.1 - - + +
336A HIS 4.9 3.2 + - - -
337A ALA* 3.3 17.0 - - + -
338A ILE* 2.9 25.6 + - - +
461A LEU* 3.8 25.6 - - + +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASP* 4.7 5.4 - - - +
177A ILE 3.1 9.4 + - - +
178A GLU* 3.4 24.6 - - + +
179A VAL* 3.0 30.9 + - - +
292A LEU* 1.3 78.7 - - - +
294A ILE* 1.3 67.1 + - - +
337A ALA* 4.4 1.7 - - - +
338A ILE* 3.3 30.5 - - + +
340A ASN* 5.1 2.2 - - + -
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 5.5 0.2 - - - +
179A VAL* 3.9 6.3 - - + +
181A LEU* 3.7 26.0 - - + -
187A LEU* 4.2 20.2 - - + -
278A LEU* 3.7 29.8 - - + -
293A ALA* 1.3 80.8 - - - +
295A LYS* 1.3 65.7 + - - +
296A VAL* 4.3 11.9 - - + -
328A ILE* 4.0 21.5 - - + -
331A MET* 4.8 2.0 - - + -
332A LEU* 3.7 32.8 - - + -
337A ALA* 5.3 0.7 - - + -
338A ILE 3.1 4.2 + - - +
339A LEU* 4.8 1.1 - - - -
340A ASN* 3.0 29.3 + - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 5.5 1.0 - - - -
51A THR* 5.8 0.6 - - - +
89A ILE* 3.4 34.7 - - + +
178A GLU* 3.4 29.2 - - + +
179A VAL 5.0 1.7 + - - +
181A LEU* 5.5 0.6 - - - +
184A ALA 4.9 0.4 + - - -
185A GLY* 3.9 25.4 + - - +
186A GLU* 3.4 10.2 - - + -
187A LEU* 2.9 32.2 + - - +
294A ILE* 1.3 80.4 - - - +
296A VAL* 1.3 61.4 + - - +
340A ASN* 3.4 11.2 - - + +
342A THR* 4.2 5.6 - - + -
380A GLU* 3.8 13.9 + - - -
1B GLC 2.8 40.1 + - - -
2B GLC 4.0 4.8 + - - -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU* 4.6 1.3 - - - -
187A LEU* 5.3 3.1 - - + -
294A ILE* 4.3 16.2 - - + -
295A LYS* 1.3 77.9 - - - +
297A SER* 1.3 74.3 + - - +
316A TYR* 3.6 22.4 - - + +
325A TYR* 4.4 17.5 - - + -
328A ILE* 4.4 16.2 - - + -
339A LEU* 4.1 29.4 - - + -
340A ASN 2.9 10.0 + - - +
341A PHE* 3.7 12.9 - - + -
342A THR* 3.2 24.6 + - - -
366A VAL* 5.5 1.3 - - + -
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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