Contacts of the strand formed by residues 747 - 755 (chain B) in PDB entry 1QAS
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 THR 747 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B LEU* 4.3 8.7 - - + +
638B GLY* 3.5 2.4 - - - -
639B GLN* 2.9 58.4 + - - +
641B LEU* 3.9 3.0 - - - +
732B HIS* 3.8 13.5 - - + -
733B VAL 3.0 15.3 - - - +
734B HIS* 3.6 35.2 - - + +
735B LEU* 4.3 3.7 - - - +
745B SER 4.1 7.8 + - - +
746B ALA* 1.3 80.3 - - - +
748B LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B ILE* 4.9 5.6 - - + -
637B SER 3.5 5.4 - - - +
638B GLY* 3.9 14.1 - - - -
639B GLN* 3.4 1.6 - - - -
641B LEU* 4.7 4.3 - - + -
656B VAL* 3.5 41.3 - - + -
684B TRP* 4.3 6.1 - - + -
702B PHE* 4.3 21.5 - - + -
704B VAL* 3.8 26.5 - - + -
731B ARG 3.7 0.2 - - - +
732B HIS* 3.4 3.8 - - - -
733B VAL* 2.8 37.3 + - + +
735B LEU* 4.2 11.7 - - + -
747B THR* 1.3 83.9 - - - +
749B PHE* 1.3 61.7 + - - +
750B VAL* 3.6 9.1 + - + +
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Residues in contact with PHE 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 3.5 12.6 - - - +
213B GLU* 3.5 35.0 - - + -
214B ILE* 3.9 13.5 - - + -
217B ALA* 4.9 3.1 - - + -
279B LEU* 4.4 8.3 - - + -
635B ILE* 4.1 0.3 - - - -
636B ILE* 3.2 49.2 + - + -
637B SER* 2.7 31.5 + - - +
639B GLN* 3.1 4.7 + - - +
730B TYR* 3.3 41.7 - + + -
731B ARG 3.7 11.4 - - - -
732B HIS* 3.3 34.1 - + - +
748B LEU* 1.3 70.2 - - - +
750B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B VAL* 4.6 5.8 - - + -
634B ARG 3.2 9.6 - - - +
635B ILE* 3.6 29.2 - - + -
636B ILE* 3.9 8.5 - - - +
702B PHE* 4.5 3.4 - - + -
730B TYR* 3.5 5.0 - - - +
731B ARG* 2.9 43.8 + - + +
733B VAL* 3.9 22.2 - - + -
748B LEU* 4.0 13.7 - - + +
749B PHE* 1.3 82.1 - - - +
751B LYS* 1.3 61.6 + - - +
752B ILE* 3.7 27.6 - - + -
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Residues in contact with LYS 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 4.5 2.4 + - - -
240B GLN* 3.6 20.8 + - - +
632B ARG 3.6 1.6 - - - +
633B VAL* 3.5 4.2 - - - +
634B ARG* 2.9 49.1 + - + +
636B ILE* 4.1 8.7 - - + -
729B GLY* 3.2 20.6 - - - +
730B TYR* 3.1 48.2 + - + +
750B VAL* 1.3 77.0 - - - +
752B ILE* 1.3 65.9 + - - +
753B SER* 5.7 3.4 - - - -
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Residues in contact with ILE 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ARG* 5.8 0.3 - - - +
286B ALA* 4.0 13.7 - - + -
631B LEU* 3.7 21.3 - - + -
632B ARG 3.5 2.7 - - - -
633B VAL* 4.5 14.1 - - + -
702B PHE* 4.7 4.0 - - + -
726B LEU* 3.8 30.5 - - + -
727B LYS 3.3 29.8 - - - +
728B GLN* 3.5 12.3 - - + +
729B GLY* 2.9 30.2 + - - +
731B ARG* 4.4 4.9 - - + -
750B VAL* 3.7 25.4 - - + -
751B LYS* 1.3 79.8 - - - +
753B SER* 1.3 66.1 + - - +
754B ILE* 4.5 1.8 - - + -
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Residues in contact with SER 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ARG 3.4 2.1 - - - +
631B LEU* 3.2 5.9 - - - +
632B ARG* 2.8 55.0 + - - +
728B GLN* 3.9 4.9 + - - +
751B LYS* 5.6 4.0 - - - -
752B ILE* 1.3 77.7 - - - +
754B ILE* 1.3 62.6 + - - +
755B GLN* 3.7 22.9 + - - +
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Residues in contact with ILE 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B GLU* 3.4 27.6 - - + +
630B ARG 3.5 3.6 - - - -
631B LEU* 3.9 15.7 - - + -
723B TRP* 3.7 38.6 - - + +
726B LEU* 4.1 30.7 - - + +
728B GLN* 2.9 35.9 + - + +
752B ILE* 4.5 1.1 - - + -
753B SER* 1.3 76.7 + - - +
755B GLN* 1.3 66.8 + - - +
756B ASP* 4.3 5.0 + - - +
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Residues in contact with GLN 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ARG* 5.7 4.0 - - - -
629B GLU* 3.4 5.4 - - - -
630B ARG* 2.9 37.9 + - + +
632B ARG* 3.3 29.7 - - - +
728B GLN* 5.0 1.9 + - - -
753B SER* 3.7 15.6 + - - +
754B ILE* 1.3 89.1 + - - +
756B ASP* 1.3 67.8 + - - +
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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