Contacts of the helix formed by residues 580 - 592 (chain B) in PDB entry 3RFU
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 SER 580 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B ASP* 1.3 83.1 + - - +
581B LYS* 1.3 55.7 + - - +
582B ARG* 2.7 40.8 + - - -
583B THR* 3.2 17.3 + - - +
584B ALA* 3.5 5.4 + - - +
599B GLU* 4.1 10.8 + - - -
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Residues in contact with LYS 581 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B ASP 3.1 1.4 + - - -
580B SER* 1.3 69.5 - - - +
582B ARG* 1.3 56.6 + - - +
583B THR 3.5 0.2 - - - -
584B ALA* 3.9 2.5 - - - -
585B GLU* 3.0 39.5 + - + +
596B VAL* 6.4 0.9 - - + -
598B ALA* 3.8 25.6 - - + +
599B GLU* 4.4 20.4 + - + +
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Residues in contact with ARG 582 (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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530B ARG* 2.8 65.3 + - - +
531B GLY* 4.4 16.3 - - - +
533B GLY* 2.6 36.9 + - - -
534B ALA 3.9 3.0 + - - -
535B SER* 4.5 7.3 - - - +
580B SER* 2.7 25.7 + - - -
581B LYS* 1.3 76.5 - - - +
583B THR* 1.3 72.5 + - + +
585B GLU* 3.4 4.3 + - - +
586B ALA* 3.0 27.5 + - - +
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Residues in contact with THR 583 (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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427B LYS* 3.6 21.7 + - - -
533B GLY* 3.9 26.9 - - - +
579B ASP* 3.6 23.6 + - - +
580B SER* 3.5 14.4 - - - +
582B ARG* 1.3 86.9 - - + +
584B ALA* 1.3 67.2 + - - +
586B ALA* 3.1 3.9 + - - +
587B VAL* 3.0 26.9 + - - +
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Residues in contact with ALA 584 (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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427B LYS* 4.3 3.8 - - + +
575B MET* 3.7 8.2 - - - +
577B THR* 4.1 15.7 - - + -
579B ASP* 5.1 0.9 - - + +
580B SER 3.5 4.9 + - - +
581B LYS* 3.8 6.1 - - - +
582B ARG 3.2 0.2 - - - -
583B THR* 1.3 82.2 + - - +
585B GLU* 1.3 57.7 + - + +
587B VAL* 3.3 10.2 - - - +
588B ALA* 3.0 32.6 + - - +
596B VAL* 5.2 7.0 - - + -
598B ALA* 3.7 29.6 - - + -
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Residues in contact with GLU 585 (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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581B LYS* 3.0 33.0 + - + +
582B ARG* 3.9 4.7 - - - +
584B ALA* 1.3 75.0 - - + +
586B ALA* 1.3 59.5 + - - +
588B ALA* 3.9 1.8 - - - +
589B GLY* 3.0 23.2 + - - -
596B VAL* 3.0 36.3 - - + +
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Residues in contact with ALA 586 (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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531B GLY 5.1 1.1 - - - +
532B LYS* 3.2 38.6 - - + +
582B ARG 3.0 12.9 + - - +
583B THR* 3.1 11.4 + - - +
585B GLU* 1.3 74.8 - - - +
587B VAL* 1.3 62.0 + - - +
589B GLY* 2.8 17.5 + - - -
590B THR* 3.0 18.4 + - - +
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Residues in contact with VAL 587 (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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427B LYS* 3.6 21.1 - - + -
431B LEU* 4.8 2.0 - - + -
432B THR* 4.0 13.7 - - + -
555B ILE* 3.6 25.1 - - + -
575B MET* 3.6 13.7 - - + -
583B THR 3.3 9.9 - - - +
584B ALA 3.3 11.9 - - - +
586B ALA* 1.3 78.2 - - - +
588B ALA* 1.3 61.2 + - - +
590B THR* 3.0 20.5 + - - -
591B LEU* 3.0 43.6 + - + +
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Residues in contact with ALA 588 (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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575B MET* 3.7 15.0 - - + -
584B ALA 3.0 21.0 + - - +
585B GLU* 3.9 6.5 - - - +
587B VAL* 1.3 78.3 - - - +
589B GLY* 1.3 61.3 + - - +
592B GLY 3.2 3.3 + - - -
593B ILE* 3.1 41.0 + - + +
596B VAL* 3.3 31.0 - - + -
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Residues in contact with GLY 589 (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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585B GLU 3.0 12.9 + - - -
586B ALA 2.8 8.4 + - - -
588B ALA* 1.3 79.2 - - - +
590B THR* 1.3 60.9 + - - +
592B GLY* 4.2 4.9 + - - -
593B ILE 4.9 1.3 - - - -
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Residues in contact with THR 590 (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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532B LYS* 5.3 13.5 - - - -
555B ILE* 4.7 7.3 - - - +
560B PRO* 5.9 1.7 - - - +
586B ALA 3.0 11.5 + - - +
587B VAL* 3.0 21.7 + - - +
589B GLY* 1.3 77.6 - - - +
591B LEU* 1.3 67.4 + - - +
592B GLY 3.5 0.2 - - - -
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Residues in contact with LEU 591 (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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431B LEU* 3.4 43.7 - - + -
555B ILE* 4.6 12.6 - - + -
559B THR* 3.7 23.8 - - + +
560B PRO* 4.0 24.3 - - + +
563B ILE* 3.6 21.6 - - + +
564B LEU* 4.3 13.3 - - - +
567B GLN* 5.1 0.2 + - - -
575B MET* 4.7 0.2 - - + -
587B VAL* 3.0 36.2 + - + +
589B GLY 3.5 0.2 - - - -
590B THR* 1.3 82.3 - - - +
592B GLY* 1.3 57.0 + - - +
593B ILE* 3.4 21.1 - - + -
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Residues in contact with GLY 592 (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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563B ILE* 5.3 0.7 - - - -
564B LEU* 5.8 1.3 - - - -
567B GLN* 3.8 21.6 + - - -
588B ALA 3.2 5.5 + - - -
589B GLY 4.2 4.8 + - - -
590B THR 3.5 2.6 - - - -
591B LEU* 1.3 77.6 - - - +
593B ILE* 1.3 65.9 + - - +
594B LYS* 3.4 17.2 + - - +
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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