Contacts of the strand formed by residues 424 - 432 (chain A) in PDB entry 3FO5
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LEU* 4.1 20.9 - - + -
364A TYR* 3.8 17.9 - - + -
417A THR* 4.6 9.4 - - - -
418A LEU 3.7 7.6 - - - +
419A GLU* 3.7 29.6 - - + -
423A PHE* 1.3 70.5 - - - +
425A SER* 1.3 60.7 + - - +
426A PHE 4.1 0.2 + - - -
549A GLN 3.7 1.1 - - - -
555A LEU* 4.5 2.7 - - + -
558A VAL* 3.8 21.4 - - + +
559A THR* 3.8 30.3 - - + -
562A VAL* 4.7 7.2 - - + -
595A GOL 2.6 48.0 + - - +
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Residues in contact with SER 425 (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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398A LEU* 4.7 4.1 - - - +
401A LYS* 5.8 0.3 + - - -
404A TRP* 4.0 16.4 - - - -
417A THR* 3.5 4.7 - - - -
418A LEU* 2.8 42.1 + - - +
420A ASP* 4.6 2.8 + - - +
423A PHE* 3.7 10.4 + - - -
424A LEU* 1.3 76.1 - - - +
426A PHE* 1.3 61.4 + - - +
548A ASN 3.2 2.5 - - - -
549A GLN* 2.7 42.8 + - - +
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Residues in contact with PHE 426 (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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2A 1PE 4.0 18.8 - - - -
404A TRP* 3.6 8.1 - - - -
415A LEU* 4.3 12.1 - - + -
416A TYR 3.3 12.8 - - - +
417A THR* 4.3 7.4 - - + -
424A LEU* 6.0 0.2 - - + -
425A SER* 1.3 75.2 - - - +
427A HIS* 1.3 70.7 + - - +
428A MET* 4.7 3.8 - - + -
546A TYR* 3.9 23.1 - + - -
547A TYR* 3.6 0.3 - - - -
548A ASN* 2.9 62.6 + - + +
558A VAL* 3.8 37.0 - - + -
562A VAL* 4.4 5.6 - - + -
569A PHE* 3.6 32.8 - + - -
595A GOL 4.0 3.4 - - - -
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Residues in contact with HIS 427 (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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404A TRP* 3.5 33.7 - + + -
415A LEU* 3.5 3.8 - - - +
416A TYR* 2.7 68.9 + + + +
426A PHE* 1.3 80.2 - - - +
428A MET* 1.3 73.4 + - - +
429A GLU* 3.4 22.8 + - + -
545A SER* 4.3 1.3 - - - -
546A TYR 3.0 15.0 - - - +
547A TYR* 3.4 48.0 + + + -
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Residues in contact with MET 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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2A 1PE 5.6 2.9 - - - +
413A VAL* 3.8 12.1 - - + -
414A ARG 3.1 7.2 - - - +
415A LEU* 3.7 32.5 - - + -
426A PHE* 4.7 10.5 - - + -
427A HIS* 1.3 75.6 - - - +
429A GLU* 1.3 62.8 + - - +
545A SER* 3.1 6.9 - - - -
546A TYR* 2.8 35.0 + - + +
569A PHE* 3.4 46.0 - - + +
570A TYR* 3.7 11.7 - - + +
573A PHE* 3.4 41.7 - - + -
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Residues in contact with GLU 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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412A GLN 4.0 1.2 - - - +
413A VAL* 3.4 3.8 - - - +
414A ARG* 2.8 50.2 + - + +
416A TYR* 3.2 34.0 + - + -
427A HIS* 3.4 19.9 + - + -
428A MET* 1.3 77.9 - - - +
430A MET* 1.3 62.8 - - - +
431A VAL* 6.2 0.4 - - + -
543A LYS* 3.7 34.4 + - + +
544A VAL 3.5 5.4 - - - -
545A SER* 3.7 14.2 + - - +
547A TYR* 5.3 0.5 + - - -
573A PHE* 3.6 2.8 - - - -
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Residues in contact with MET 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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412A GLN 4.3 8.5 - - - +
413A VAL* 4.0 22.2 - - + -
429A GLU* 1.3 76.2 - - - +
431A VAL* 1.3 63.7 + - - +
432A VAL* 3.6 28.3 - - + -
543A LYS* 3.5 5.1 - - - +
544A VAL* 2.8 50.8 + - + +
573A PHE* 3.4 49.1 - - + +
574A LYS* 5.6 0.4 - - - -
576A CYS* 4.1 9.9 - - + -
577A GLU* 3.8 23.3 - - - +
580A LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 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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412A GLN 5.1 2.4 + - - -
429A GLU* 6.2 0.7 - - + -
430A MET* 1.3 79.8 - - - +
432A VAL* 1.3 68.3 + - - +
537A GLU* 4.7 10.1 - - + -
541A LEU* 3.6 31.4 - - + -
542A THR 3.3 14.6 - - - +
543A LYS* 4.2 23.8 - - + +
577A GLU* 4.5 6.2 - - - +
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Residues in contact with VAL 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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430A MET* 3.6 39.7 - - + -
431A VAL* 1.3 79.9 - - - +
433A HIS* 1.3 62.5 + - - +
434A VAL* 3.0 35.0 + - + +
541A LEU* 3.5 7.6 - - - +
542A THR* 2.9 32.4 + - - +
544A VAL* 3.9 10.1 - - + -
577A GLU* 4.1 24.5 - - + +
580A LEU* 4.3 9.9 - - + -
581A LEU* 4.2 6.3 - - + -
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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