Contacts of the strand formed by residues 432 - 443 (chain B) in PDB entry 2O5C
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 GLY 432 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B TRP* 4.7 8.5 - - - -
428B ASP* 3.7 5.5 - - - +
429B ILE 3.0 33.0 + - - +
430B ALA 3.1 3.6 + - - -
431B LYS* 1.3 80.4 - - - +
433B LYS* 1.3 65.3 + - - +
434B PHE* 3.6 10.4 - - - -
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Residues in contact with LYS 433 (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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240B TRP* 3.2 12.7 - - - +
241B GLN* 2.8 53.3 + - + +
277B THR* 5.7 3.6 - - - -
427B LEU 4.1 6.1 - - - +
428B ASP* 2.8 32.1 + - - -
431B LYS 4.7 7.4 + - - +
432B GLY* 1.3 72.4 - - - -
434B PHE* 1.3 57.0 + - - +
435B VAL* 5.8 2.2 - - + -
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Residues in contact with PHE 434 (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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224B VAL* 4.0 5.4 - - + -
226B ALA* 3.7 26.7 - - + -
238B ALA* 4.2 10.1 - - + -
239B ILE 3.3 6.1 - - - -
240B TRP* 3.4 48.7 - + + -
265B VAL* 4.1 7.0 - - + -
269B ILE* 3.7 41.1 - - + -
426B GLU* 3.5 1.2 - - - +
427B LEU* 2.9 37.3 + - + +
429B ILE* 3.7 33.7 - - + -
432B GLY* 3.6 13.2 - - - -
433B LYS* 1.3 76.8 - - - +
435B VAL* 1.3 68.7 + - - +
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Residues in contact with VAL 435 (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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238B ALA* 3.4 2.6 - - - -
239B ILE* 2.7 43.5 + - - +
241B GLN* 3.6 30.5 - - + +
424B VAL* 3.8 17.7 - - + -
425B ILE 3.5 3.4 - - - +
426B GLU* 4.1 19.7 - - + +
433B LYS* 5.4 2.0 - - + -
434B PHE* 1.3 82.0 - - - +
436B ALA* 1.3 60.5 + - - +
437B LYS* 3.7 33.0 - - + -
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Residues in contact with ALA 436 (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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236B PHE* 3.8 25.4 - - + -
237B THR 3.4 24.7 - - - +
238B ALA* 4.0 3.3 - - + +
424B VAL* 3.4 5.5 - - - +
425B ILE* 3.0 37.5 + - + +
435B VAL* 1.3 73.6 - - - +
437B LYS* 1.3 62.4 + - - +
464B LEU* 3.7 15.3 - - + +
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Residues in contact with LYS 437 (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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422B LYS* 3.5 28.5 - - + +
423B CYS 3.4 4.7 - - - +
424B VAL* 4.0 22.9 - - + -
435B VAL* 3.7 23.3 + - + +
436B ALA* 1.3 79.0 - - - +
438B ALA* 1.3 61.9 + - - +
460B ASP* 4.3 11.5 - - - +
461B GLY* 4.2 13.5 - - - -
462B THR 4.6 2.1 + - - +
464B LEU* 3.8 5.3 - - - +
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Residues in contact with ALA 438 (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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421B ARG 3.7 1.0 - - - +
422B LYS* 3.4 4.6 - - - +
423B CYS* 2.8 38.2 + - + +
437B LYS* 1.3 75.2 - - - +
439B ARG* 1.3 62.2 + - - +
440B PHE* 4.2 8.3 - - + -
460B ASP* 3.3 11.7 - - - +
462B THR 3.5 26.7 - - - +
463B PRO* 4.4 4.0 - - + -
464B LEU* 4.0 13.0 - - + +
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Residues in contact with ARG 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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284B GLU* 2.6 37.1 + - - +
285B SER 5.5 1.2 + - - -
286B GLU* 5.3 4.9 + - - +
420B PHE* 3.6 52.3 - - + +
421B ARG 3.3 6.1 - - - +
422B LYS* 4.1 20.0 - - + +
438B ALA* 1.3 75.3 - - - +
440B PHE* 1.3 60.9 + - - +
458B GLU* 4.0 21.4 + - - +
459B ASN* 3.2 7.4 - - - +
460B ASP* 2.9 45.4 + - + +
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Residues in contact with PHE 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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420B PHE* 3.8 3.6 - - - -
421B ARG* 2.8 35.0 + - + +
438B ALA* 4.3 5.6 - - + -
439B ARG* 1.3 83.5 - - - +
441B LEU* 1.3 67.9 + - - +
442B ALA* 4.2 1.9 - - - +
459B ASN* 3.6 31.6 - - + -
460B ASP 3.7 10.5 - - - -
461B GLY 3.4 26.2 - - - -
462B THR 4.0 1.6 - - - -
463B PRO* 3.6 42.2 - - + -
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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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418B ALA* 3.7 22.2 - - + -
419B VAL 3.7 4.9 - - - +
420B PHE* 3.4 18.9 - - + -
440B PHE* 1.3 77.2 - - - +
442B ALA* 1.3 59.6 + - - +
443B GLU 3.5 22.0 - - - +
444B ALA* 3.9 19.3 - - + +
447B ARG* 3.9 10.3 - - - -
455B ARG* 3.6 43.5 - - + +
456B ASP* 4.5 4.5 - - - +
459B ASN* 3.0 23.2 + - - +
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Residues in contact with ALA 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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419B VAL* 2.7 17.1 + - + +
421B ARG* 3.6 45.2 + - + +
440B PHE 3.3 3.3 + - - +
441B LEU* 1.3 75.0 - - - +
443B GLU* 1.3 67.0 + - + +
444B ALA 4.1 1.1 + - - -
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Residues in contact with GLU 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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283B ARG* 3.2 28.9 + - - +
417B ASP 5.0 2.6 - - - +
418B ALA* 3.3 0.9 - - - -
419B VAL* 2.8 55.5 + - + +
421B ARG* 6.2 1.1 - - - +
441B LEU* 3.5 4.7 - - - +
442B ALA* 1.3 82.6 - - + +
444B ALA* 1.3 64.6 + - - +
445B GLY 3.3 4.5 + - - +
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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