Contacts of the strand formed by residues 298 - 303 (chain B) in PDB entry 6QNW
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 LEU 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A GLU* 4.3 2.5 - - - +
297B GLU* 1.3 73.6 - - - +
299B SER* 1.3 60.5 + - - +
300B PHE* 3.5 33.0 - - + -
452B ASN* 3.3 2.2 - - - +
453B ALA 3.2 27.5 + - - +
454B PRO 4.9 1.8 - - - +
455B ASN* 4.8 7.0 - - - +
456B HIS* 3.9 33.7 - - + +
459B ILE* 3.2 41.3 - - + +
486B ARG* 3.8 30.5 - - - +
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Residues in contact with SER 299 (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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289B MET 3.6 12.0 + - - -
290B MET* 4.5 7.7 - - - +
297B GLU* 3.6 17.6 + - - +
298B LEU* 1.3 73.0 - - - +
300B PHE* 1.3 64.2 + - - +
450B ILE* 4.6 2.2 - - - -
452B ASN* 2.9 36.5 + - - +
486B ARG* 3.5 8.1 + - - +
487B THR* 2.7 44.3 + - - -
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A GLU* 3.4 49.8 - - + -
298B LEU* 3.5 21.9 + - + -
299B SER* 1.3 85.2 - - - +
301B THR* 1.3 61.8 + - - +
450B ILE* 3.5 1.0 - - - -
451B VAL* 2.9 39.0 + - + +
456B HIS* 3.6 17.7 - + - -
459B ILE* 4.1 26.9 - - + -
484B ILE* 4.1 19.3 - - + -
485B ASN 3.4 6.1 - - - +
486B ARG* 3.5 27.8 - - + -
487B THR* 3.8 0.4 - - - -
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Residues in contact with THR 301 (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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300B PHE* 1.3 70.8 - - - +
302B ILE* 1.3 64.4 + - - +
448B ALA* 5.5 0.2 - - + -
449B LEU 3.2 16.6 - - - +
450B ILE* 3.5 18.3 - - + +
484B ILE* 3.5 0.3 - - - -
485B ASN* 2.9 43.8 + - - +
486B ARG 4.6 0.7 - - - -
487B THR* 3.0 34.3 + - - +
488B GLY 4.5 0.6 + - - -
489B THR 5.0 0.2 - - - -
490B PHE* 3.7 42.4 - - + -
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Residues in contact with ILE 302 (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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681A PHE* 4.9 13.2 - - + -
300B PHE 4.8 4.0 - - - +
301B THR* 1.3 77.0 - - - +
303B THR* 1.3 63.1 + - - +
304B GLY* 5.1 2.7 - - - -
447B PHE* 3.9 27.1 - - + -
448B ALA* 3.6 4.3 - - - +
449B LEU* 2.9 53.7 + - + +
451B VAL* 5.0 4.9 - - + -
463B VAL* 5.0 19.3 - - + -
466B PHE* 4.9 4.7 - - + -
477B MET* 5.1 7.9 - - + -
482B SER* 6.1 0.4 - - - -
483B TYR 3.2 11.7 - - - +
484B ILE* 3.5 30.1 - - + -
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Residues in contact with THR 303 (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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301B THR 4.2 0.6 + - - -
302B ILE* 1.3 71.6 - - - +
304B GLY* 1.3 64.6 + - - +
447B PHE 4.3 1.6 - - - -
448B ALA* 4.9 0.2 - - - +
481B LYS 5.3 0.2 - - - -
482B SER* 3.3 5.8 - - - -
483B TYR* 2.9 57.8 + - + +
485B ASN* 5.4 0.4 + - - -
490B PHE* 3.2 14.8 - - - +
491B GLU* 3.0 67.0 + - + +
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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