Contacts of the strand formed by residues 427 - 431 (chain A) in PDB entry 6CM1
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 THR 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A TYR* 3.9 18.2 - - + -
419A LEU 3.6 8.1 - - - +
420A PHE* 4.0 7.9 - - - +
426A LYS* 1.3 74.9 - - - +
428A TYR* 1.3 73.3 + - - +
429A PHE* 3.6 30.7 - - + -
437A ARG* 3.6 3.1 - - - +
438A PHE* 2.7 49.1 + - - +
440A GLU* 2.7 33.7 + - - +
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Residues in contact with TYR 428 (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 ALA* 3.1 7.0 - - - +
419A LEU* 2.7 56.3 + - + +
421A TRP* 3.8 34.8 + + + -
424A ASN* 5.2 2.3 + - - -
426A LYS* 6.5 0.4 - - + -
427A THR* 1.3 80.4 - - - +
429A PHE* 1.3 60.9 + - - +
430A PHE* 4.0 18.8 - + + -
435A TYR* 4.3 13.4 - + - -
436A TYR 3.5 13.0 - - - +
437A ARG* 3.8 39.0 + - + -
449A TYR* 4.7 3.1 + - - -
456A TRP* 3.2 40.1 - + - -
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Residues in contact with PHE 429 (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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372A TYR* 3.5 24.7 - + - -
382A PHE* 3.7 23.6 - + - -
406A LEU* 3.7 12.6 - - + -
410A LEU* 3.5 37.5 - - + -
411A PRO* 4.8 5.4 - - + -
415A ILE* 4.2 17.7 - - + -
417A ALA 3.7 4.5 - - - -
418A ALA* 3.8 19.5 - - + -
427A THR* 3.6 10.1 - - + -
428A TYR* 1.3 77.8 - - - +
430A PHE* 1.4 62.7 + - - +
435A TYR* 3.3 6.2 - - - +
436A TYR* 3.0 53.5 + - + -
438A PHE* 3.6 26.5 - + + -
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Residues in contact with PHE 430 (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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411A PRO* 5.0 0.9 - - - +
415A ILE* 3.8 5.9 - - - +
416A ASP* 2.9 24.8 + - + -
417A ALA* 2.8 37.6 + - + +
418A ALA 4.5 1.3 - - - -
419A LEU* 3.9 14.6 - - + -
428A TYR* 4.0 20.4 - - + -
429A PHE* 1.4 73.3 - - - +
431A ARG* 1.3 61.6 + - - +
434A LYS 3.9 2.0 - - - +
435A TYR* 3.7 25.1 - - + -
436A TYR* 5.4 0.4 - - - -
453A ILE* 4.2 10.3 - - + -
456A TRP* 4.1 20.0 - + - -
459A ILE* 6.0 0.9 - - + -
463A PRO* 3.5 33.7 - - + -
466A SER* 3.5 20.0 - - - -
477A PHE* 3.7 24.9 - + - -
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Residues in contact with ARG 431 (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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411A PRO* 4.2 16.6 - - + -
413A ASP* 2.7 40.9 + - - +
414A LYS* 3.3 52.2 + - - +
416A ASP* 3.2 30.1 + - - -
429A PHE 4.2 0.4 + - - -
430A PHE* 1.3 75.0 - - - +
432A GLY* 1.4 62.4 - - - +
433A ASN 3.4 0.2 + - - -
434A LYS* 2.9 32.3 + - + +
436A TYR* 4.7 6.0 - - + +
464A ARG* 6.0 0.2 - - - +
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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