Contacts of the strand formed by residues 429 - 437 (chain B) in PDB entry 4X7C
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 GLU 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B PRO* 3.4 22.0 - - + +
425B THR* 3.4 25.1 + - - -
426B PHE* 3.2 39.5 + - + +
427B PRO 3.2 2.8 - - - +
428B GLY* 1.3 80.5 + - - +
430B GLN* 1.3 68.3 + - - +
490B LYS* 3.8 19.4 + - - +
492B HIS* 4.4 5.4 + - - -
498B THR* 3.0 27.2 + - - +
499B VAL 3.3 10.5 - - - +
500B ALA* 5.4 1.6 - - + -
502B THR* 5.7 0.3 - - - +
527B LEU* 4.6 6.2 - - + +
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Residues in contact with GLN 430 (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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251B THR* 3.1 22.7 + - - +
252B GLY 3.4 19.4 - - - +
253B PRO* 3.2 21.4 - - + +
424B PRO* 4.1 8.1 - - + -
429B GLU* 1.3 77.2 - - - +
431B LEU* 1.3 63.1 + - - +
498B THR* 3.1 9.1 - - - -
499B VAL* 2.8 33.9 + - + +
501B HIS* 3.0 28.6 + - - +
502B THR* 3.5 3.6 - - + -
503B GLY 2.8 42.3 + - - -
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Residues in contact with LEU 431 (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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251B THR* 2.8 27.4 + - - -
252B GLY 4.1 3.6 + - - +
254B SER* 3.7 18.6 + - - +
259B VAL* 4.1 5.8 - - + -
422B VAL* 4.0 32.5 - - + +
423B ALA 4.4 4.9 - - - -
424B PRO* 3.8 12.2 - - + +
430B GLN* 1.3 73.8 - - - +
432B LEU* 1.3 59.8 + - - +
433B PHE* 3.5 40.4 + - + -
452B LEU* 5.3 2.5 - - + -
496B TYR* 3.5 35.9 - - + -
497B VAL 3.5 6.3 - - - +
498B THR* 3.9 7.2 - - + -
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Residues in contact with LEU 432 (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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249B LEU* 4.2 10.8 - - + -
250B PHE 3.8 12.1 - - - +
251B THR* 4.6 3.1 - - - -
430B GLN 3.5 0.6 + - - -
431B LEU* 1.3 72.8 - - - +
433B PHE* 1.3 67.3 + - - +
434B PHE* 4.1 16.3 + - + -
451B CYS 4.6 1.2 - - - +
452B LEU* 4.7 5.5 - - - +
487B PHE* 4.3 6.7 - - + -
497B VAL* 2.7 50.2 + - + +
499B VAL* 3.9 23.8 - - + -
507B LEU* 3.9 32.3 - - + -
515B PHE* 4.1 28.3 - - + -
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Residues in contact with PHE 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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249B LEU* 3.4 8.3 - - - +
250B PHE* 2.7 60.9 + + + +
252B GLY* 4.2 16.2 - - - -
253B PRO 5.9 0.2 - - - -
254B SER* 4.7 5.2 - - - -
257B PHE* 5.3 3.8 - + - -
259B VAL* 4.2 7.9 - - + -
403B TRP* 3.7 27.1 - + - -
431B LEU* 3.5 42.2 - - + -
432B LEU* 1.3 75.7 - - - +
434B PHE* 1.3 62.9 + - - +
435B ARG 3.8 0.2 - - - -
450B ASP* 3.7 36.3 - - + +
451B CYS 3.9 3.1 - - - -
452B LEU* 4.0 22.4 - - + -
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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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234B VAL* 5.3 1.8 - - + -
237B MET* 5.0 2.7 - - + -
239B ASN* 3.9 1.6 + - - -
246B LEU* 3.8 20.4 - - + -
248B LYS 3.9 2.9 - - - -
249B LEU* 3.4 26.9 - - + -
432B LEU* 4.3 11.2 - - + -
433B PHE* 1.3 72.8 - - - +
435B ARG* 1.3 60.4 + - - +
449B LEU 3.8 1.0 - - - +
450B ASP* 3.6 1.7 - - - -
451B CYS* 3.0 51.9 + - - +
452B LEU 3.3 28.9 - - - -
454B PRO* 3.8 32.8 - - + -
457B TRP* 4.1 19.3 - + - -
497B VAL* 4.2 15.5 - - + -
515B PHE* 3.9 22.4 - + - -
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Residues in contact with ARG 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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246B LEU* 3.9 1.5 - - - +
247B GLU* 2.9 24.9 + - - +
248B LYS* 2.8 52.5 + - + +
250B PHE* 3.4 55.8 - - + +
402B GLN* 4.8 1.0 - - - +
434B PHE* 1.3 73.4 - - - +
436B SER* 1.3 73.4 + - - +
448B ASP* 4.0 33.0 + - - +
449B LEU 3.5 5.4 - - - +
450B ASP* 2.7 40.0 + - - +
506B ASP* 4.5 4.8 + - - -
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Residues in contact with SER 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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239B ASN* 2.9 28.1 + - - +
244B ILE* 3.6 17.9 - - - -
245B PRO 2.6 28.0 + - - -
246B LEU* 3.4 10.4 - - - -
247B GLU* 3.9 7.4 - - - -
435B ARG* 1.3 79.4 - - - +
437B THR* 1.3 63.5 + - - +
438B MET 4.0 0.7 - - - -
447B MET 3.6 0.7 - - - +
448B ASP* 4.0 2.1 - - - +
449B LEU* 3.0 29.2 + - - +
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Residues in contact with THR 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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244B ILE* 4.0 6.7 - - - +
247B GLU* 2.7 37.1 + - - +
248B LYS* 3.7 9.5 + - - -
436B SER* 1.3 73.0 + - - +
438B MET* 1.3 67.7 + - - +
439B PRO* 3.5 5.5 - - - +
447B MET* 3.5 31.4 - - + +
448B ASP* 5.2 4.2 + - - +
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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