Contacts of the strand formed by residues 431 - 438 (chain A) in PDB entry 5E8M
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 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A VAL* 3.8 27.6 - - + +
427A LYS 5.7 3.9 + - - +
428A ARG* 4.0 14.9 - - - +
429A ARG 4.7 0.4 - - - +
430A LYS* 1.3 76.8 - - - +
432A ARG* 1.3 59.2 + - - +
433A VAL* 3.5 27.8 + - + -
454A ALA* 4.9 1.3 - - + -
455A ILE 3.4 12.1 - - - +
456A ASN* 4.0 25.1 - - + +
458A HIS* 3.9 11.7 + - + +
462A LYS* 4.2 18.8 - - + -
464A LEU* 3.9 21.1 - - + -
524A LEU* 4.2 8.5 - - + -
610A EDO 4.2 2.3 + - - -
4B VAL* 4.8 10.1 - - + -
6B LEU* 5.1 0.2 - - + -
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Residues in contact with ARG 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 3.9 9.3 + - - +
316A LEU* 3.8 19.1 - - - +
317A ASP* 2.9 34.8 + - - +
320A ILE* 4.7 0.8 - - - +
367A ASP* 2.8 45.5 + - - +
371A LEU* 4.1 11.7 - - - +
428A ARG 4.6 3.0 + - - -
429A ARG* 3.0 32.6 + - - +
430A LYS 4.3 2.5 - - - +
431A LEU* 1.3 71.0 - - - +
433A VAL* 1.3 63.2 + - - +
434A TYR* 4.2 6.3 - - + -
453A TYR 4.0 0.2 - - - +
454A ALA* 3.1 5.5 - - - +
455A ILE* 2.9 56.2 + - + +
457A LEU* 4.6 3.6 - - - -
610A EDO 3.5 25.5 - - - -
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ALA* 3.6 41.3 + - + +
422A SER* 3.7 15.9 - - - +
423A VAL* 4.3 7.0 - - + +
431A LEU* 3.5 23.8 - - + -
432A ARG* 1.3 79.0 - - - +
434A TYR* 1.3 73.5 + - - +
452A LEU* 4.3 6.7 - - + -
453A TYR 3.5 3.8 - - - +
454A ALA* 3.9 13.9 - - + -
464A LEU* 4.7 3.6 - - + -
610A EDO 3.0 20.6 + - - +
6B LEU* 4.2 13.5 - - + -
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU 4.7 0.2 - - - -
367A ASP* 2.6 35.0 + - - -
370A GLY* 3.4 34.5 - - - +
371A LEU* 3.3 30.6 - - + +
374A ARG* 4.7 11.2 - - + -
420A MET* 6.0 0.2 - - - +
421A ALA* 4.4 3.4 - - - +
432A ARG* 4.2 11.2 - - + -
433A VAL* 1.3 80.7 - - - +
435A LEU* 1.3 62.0 + - - +
436A HIS* 5.0 1.8 - - + +
452A LEU* 3.3 8.9 - - - +
453A TYR* 2.9 73.6 + + + +
454A ALA* 5.6 0.2 - - - -
455A ILE* 4.7 4.9 - - + -
610A EDO 3.4 22.9 - - - -
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A VAL* 4.4 0.2 - - - +
419A LEU* 2.8 48.6 + - + +
420A MET* 3.6 30.3 - - - +
421A ALA* 4.0 7.1 - - + +
434A TYR* 1.3 76.5 - - - +
436A HIS* 1.3 64.2 - - - +
450A LEU* 4.1 20.6 - - + -
451A THR 3.6 17.7 - - - +
452A LEU* 3.9 18.2 - - + +
534A ILE* 5.0 0.2 - - + -
8B PHE* 3.7 38.1 - - + -
10B THR* 4.1 10.5 - - + -
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Residues in contact with HIS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A GLY 5.2 0.8 + - - -
373A ALA* 3.6 29.4 - - + +
410A PHE* 4.7 3.8 - + - -
414A VAL* 3.2 24.0 - - + +
415A GLY 3.0 19.9 + - - +
417A LYS 3.3 13.8 + - - +
418A VAL* 3.8 17.7 - - + +
419A LEU* 4.1 8.3 - - - +
434A TYR* 5.0 1.1 - - + +
435A LEU* 1.3 82.4 - - - +
437A CYS* 1.3 65.1 + - - +
450A LEU* 3.6 6.4 - - - +
451A THR* 2.8 36.9 + - - +
453A TYR* 2.9 32.6 + + - -
17B VAL* 4.9 5.4 - - + -
21B PHE* 5.3 0.7 - + - -
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Residues in contact with CYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU 4.4 0.2 - - - +
414A VAL* 4.4 0.3 - - - -
415A GLY* 2.8 28.8 + - - -
417A LYS* 3.0 38.9 + - + +
419A LEU* 4.0 9.9 - - - +
436A HIS* 1.3 74.1 - - - +
438A THR* 1.3 66.3 + - - +
440A THR* 6.3 0.7 - - + -
449A ASP 3.7 1.8 - - - -
450A LEU* 4.5 0.4 - - - +
451A THR* 4.1 0.6 + - - -
541A ALA 4.4 1.6 - - - -
542A CYS* 2.1 62.6 - - + +
612A EDO 5.9 0.4 - - - +
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Residues in contact with THR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.6 5.6 - - - +
415A GLY* 4.0 0.2 - - - -
436A HIS 3.6 1.4 + - - -
437A CYS* 1.3 77.8 - - - +
439A ASN* 1.3 77.2 - - + +
440A THR* 3.1 13.2 + - - +
442A ASN* 5.1 0.4 - - + -
445A TYR* 3.9 35.4 - - + -
446A LYS 5.5 0.9 - - - -
449A ASP* 2.9 27.8 + - - +
450A LEU 3.0 18.7 + - - -
451A THR* 2.9 23.8 + - - +
533A VAL* 3.8 3.9 - - + +
612A EDO 4.3 2.3 + - - -
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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