Contacts of the strand formed by residues 436 - 443 (chain B) in PDB entry 6T2C
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 TYR 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B ARG* 5.5 1.0 - - - +
432B LEU* 3.7 32.6 - - + +
434B ARG* 3.1 54.1 + - + +
435B THR* 1.3 89.2 - - - +
437B TRP* 1.3 71.3 + - - +
438B TRP* 4.1 12.1 - + - -
451B ILE* 4.7 5.8 - - + -
452B ASN 3.4 12.3 - - - +
453B GLY* 4.9 0.2 - - - -
458B ASP* 3.7 25.6 - - - +
461B GLN* 4.2 16.7 + - + +
462B GLY* 3.7 30.1 - - - -
465B HIS* 3.8 20.9 - + + +
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Residues in contact with TRP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MET* 3.7 23.8 - - + +
297B GLU* 3.3 33.8 + - + -
427B GLY 3.8 11.0 - - - +
428B GLN 4.5 1.1 - - - -
429B ARG* 3.5 63.4 - - + +
432B LEU* 4.4 6.1 - - - -
434B ARG 5.1 3.6 - - - -
435B THR* 4.4 12.6 - - - -
436B TYR* 1.3 85.2 - - - +
438B TRP* 1.3 67.4 + - - +
451B ILE* 3.4 3.3 - - - +
452B ASN* 2.9 55.4 + - + +
453B GLY* 4.7 2.7 - - - -
454B HIS* 4.6 20.0 - + - -
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Residues in contact with TRP 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MET* 4.2 6.1 - - - +
423B VAL* 3.5 23.5 + - + -
424B LEU* 3.6 15.8 + - - +
426B LEU* 4.7 8.3 - - + -
427B GLY* 2.9 39.9 + - - +
428B GLN* 5.7 0.5 - - - +
432B LEU* 4.3 5.6 - - + -
436B TYR* 4.1 22.7 - + - -
437B TRP* 1.3 80.5 - - - +
439B ASP* 1.3 67.4 + - - +
449B LEU* 3.7 24.9 - - + -
450B ILE 3.1 13.5 - - - +
451B ILE* 4.0 11.4 - - + -
462B GLY* 3.4 26.7 - - - -
465B HIS* 3.3 31.4 - + - -
466B PHE* 3.7 29.3 - + + -
469B THR* 5.2 1.1 - - - -
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Residues in contact with ASP 439 (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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268B GLN* 3.0 36.4 + - - +
285B VAL* 5.1 8.5 - - + +
288B LYS* 4.2 24.9 + - - +
289B MET* 3.7 25.4 - - + +
424B LEU* 4.1 7.4 - - - +
438B TRP* 1.3 81.1 - - - +
440B GLY* 1.3 62.9 + - - +
449B LEU* 3.3 11.3 - - - +
450B ILE* 2.9 30.8 + - - -
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Residues in contact with GLY 440 (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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268B GLN* 3.3 26.7 - - - +
285B VAL* 4.7 8.2 - - - +
424B LEU* 3.8 8.3 - - - +
439B ASP* 1.3 85.1 + - - +
441B LEU* 1.3 71.2 + - - +
448B ALA 3.3 9.4 - - - -
450B ILE* 4.3 12.6 - - - -
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Residues in contact with LEU 441 (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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267B GLU 4.1 7.0 - - - +
268B GLN* 3.7 19.5 - - - +
269B SER 5.0 0.7 - - - +
270B GLY* 5.2 4.0 - - - +
278B LYS* 6.3 0.2 - - + -
281B LYS* 4.4 12.6 - - + +
282B LEU* 3.9 41.5 - - + +
285B VAL* 3.8 27.1 - - + -
424B LEU* 3.7 4.9 - - - +
440B GLY* 1.3 85.3 - - - +
442B GLN* 1.3 60.6 + - - +
447B PHE* 3.4 4.7 - - - +
448B ALA* 2.9 37.6 + - + +
450B ILE* 6.3 0.4 - - + -
490B PHE* 5.7 1.3 - - + -
492B PHE* 4.0 28.0 - - + -
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Residues in contact with GLN 442 (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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268B GLN 3.3 10.4 + - - +
270B GLY 3.4 14.7 + - - -
306B ASN* 4.3 13.2 + - - +
309B TRP* 3.7 28.5 - - - -
416B SER 4.8 1.0 + - - -
417B THR* 3.5 23.6 - - - +
420B GLY* 3.7 30.8 - - - +
421B VAL* 4.6 2.0 - - + -
424B LEU* 3.8 16.3 - - + +
441B LEU* 1.3 76.0 - - - +
443B SER* 1.3 63.9 + - - +
444B SER 4.0 11.3 + - - -
445B ASP* 4.4 3.0 - - - +
446B ASP 3.5 4.5 - - - -
447B PHE* 3.8 17.1 - - - +
466B PHE* 5.7 3.1 - - - -
475B ILE* 5.3 4.6 - - - +
492B PHE* 4.0 1.6 - - - -
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Residues in contact with SER 443 (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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270B GLY* 4.0 7.8 - - - -
271B LEU* 2.7 36.3 - - - +
278B LYS* 4.7 4.0 + - - -
417B THR* 4.5 0.7 - - - -
442B GLN* 1.3 73.6 - - - +
444B SER* 1.3 57.4 + - - +
445B ASP 2.6 2.6 + - - -
446B ASP* 2.5 44.7 + - - +
492B PHE* 3.2 26.9 - - - -
493B THR* 4.2 9.4 - - - +
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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