Contacts of the helix formed by residues 564 - 580 (chain D) in PDB entry 3RCW
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 564 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565D THR* 1.3 62.1 + - - +
566D PRO* 3.1 20.4 - - + +
567D LEU* 3.0 16.3 + - - +
568D THR* 2.9 30.5 + - - -
619D GLN* 6.1 2.0 - - - -
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Residues in contact with THR 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D LEU* 1.3 77.7 - - - +
566D PRO* 1.4 64.0 - - - +
568D THR* 3.3 10.0 + - - -
569D VAL* 3.1 35.0 + - - +
619D GLN* 6.1 0.7 - - - +
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Residues in contact with PRO 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A ALA 5.4 5.5 - - - -
564D LEU* 3.4 15.7 - - + +
565D THR* 1.4 91.2 - - - +
567D LEU* 1.3 62.9 + - - +
569D VAL* 3.4 7.7 + - + +
570D LEU* 3.1 22.9 + - - +
673D ILE* 5.2 23.4 - - + +
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Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D LEU* 3.0 19.6 + - - +
566D PRO* 1.3 73.6 - - - +
568D THR* 1.3 68.2 + - - +
570D LEU* 3.0 20.2 + - + +
571D LEU* 2.9 41.2 + - + +
621D TYR 3.7 11.7 - - - +
622D LYS 3.7 9.4 - - - +
623D ASN* 3.4 33.9 - - - +
624D LEU* 4.1 19.7 - - + +
670D VAL* 4.9 6.3 - - + -
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Residues in contact with THR 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D LEU 2.9 16.0 + - - -
565D THR* 3.5 11.7 - - - -
566D PRO 3.3 0.2 - - - -
567D LEU* 1.3 76.3 - - - +
569D VAL* 1.3 62.5 + - + +
571D LEU* 3.4 1.5 + - - -
572D ARG* 3.1 48.5 + - - +
616D LEU* 4.0 24.9 + - + +
617D GLU* 5.0 2.0 - - - +
619D GLN* 3.3 40.9 + - - +
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Residues in contact with VAL 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A GLU 4.6 3.4 - - - +
678A ALA* 4.0 30.9 + - + +
565D THR* 3.1 20.2 + - - +
566D PRO* 3.9 7.2 - - + +
567D LEU 3.2 0.2 - - - -
568D THR* 1.3 77.3 - - - +
570D LEU* 1.3 64.3 + - - +
572D ARG* 3.5 21.4 + - + +
573D SER* 3.4 20.3 + - - +
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Residues in contact with LEU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A LEU* 3.9 37.2 - - + +
678A ALA 5.3 11.1 - - - +
566D PRO 3.1 16.3 + - - +
567D LEU* 3.0 16.4 + - + +
569D VAL* 1.3 78.1 - - - +
571D LEU* 1.3 61.4 + - + +
573D SER* 3.1 7.6 + - - -
574D VAL* 2.9 35.8 + - + +
624D LEU* 5.4 0.9 - - + -
666D ALA* 4.3 9.2 - - + +
669D GLU* 4.5 16.6 - - + -
670D VAL* 3.7 30.3 - - + -
673D ILE* 4.8 11.2 - - + -
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Residues in contact with LEU 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU* 2.9 42.3 + - + +
568D THR* 5.3 0.2 - - - -
570D LEU* 1.3 77.0 - - + +
572D ARG* 1.3 56.4 + - - +
574D VAL* 3.1 8.1 + - + +
575D LEU* 2.7 37.6 + - - +
616D LEU* 3.8 20.9 - - + -
621D TYR* 4.0 26.9 - - + +
623D ASN 4.7 1.3 - - - +
624D LEU* 3.5 33.7 - - + -
627D PHE* 3.7 32.6 - - + -
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Residues in contact with ARG 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D THR* 3.1 36.8 + - - +
569D VAL* 3.6 22.2 - - + +
571D LEU* 1.3 75.0 - - - +
573D SER* 1.3 59.3 + - - +
575D LEU* 3.2 2.8 + - - +
576D ASP* 2.9 37.1 + - - +
613D ARG* 4.6 6.6 + - - +
616D LEU* 3.8 15.6 - - + +
617D GLU* 3.5 36.8 + - - +
619D GLN* 5.4 2.0 - - - +
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Residues in contact with SER 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A GLY 4.0 9.1 + - - -
675A LEU* 3.7 18.4 - - - -
677A GLU 3.9 16.0 + - - -
569D VAL* 3.4 9.7 + - - +
570D LEU* 3.1 10.8 + - - -
572D ARG* 1.3 77.2 - - - +
574D VAL* 1.3 65.6 + - - +
576D ASP* 3.5 9.1 + - - +
577D GLN* 3.0 31.1 + - - +
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Residues in contact with VAL 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A LEU* 3.6 17.7 - - + -
570D LEU* 2.9 23.5 + - + +
571D LEU* 3.6 13.0 - - + +
573D SER* 1.3 74.3 - - - +
575D LEU* 1.3 59.1 + - - +
577D GLN* 3.2 2.6 + - - +
578D LEU* 2.9 31.4 + - + +
627D PHE* 3.8 23.6 - - + -
662D VAL* 3.7 21.5 - - + -
663D LEU* 3.9 15.3 - - + -
666D ALA* 3.6 27.4 - - + -
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Residues in contact with LEU 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D LEU 2.7 21.1 + - - +
572D ARG* 3.6 4.5 - - - +
574D VAL* 1.3 72.0 - - - +
576D ASP* 1.3 52.8 + - - +
578D LEU* 3.0 6.2 + - + +
579D GLN* 2.8 34.8 + - - +
609D PHE* 3.6 36.1 - - + +
612D MET* 4.2 10.8 - - + -
613D ARG* 3.5 61.0 - - + +
616D LEU* 4.0 12.6 - - + -
627D PHE* 4.0 21.8 - - + -
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Residues in contact with ASP 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ARG* 2.9 22.3 + - - +
573D SER* 3.6 8.3 - - - +
575D LEU* 1.3 75.7 - - - +
577D GLN* 1.3 61.6 + - + +
579D GLN* 3.4 4.6 + - - +
580D ASP* 3.1 31.6 + - - +
613D ARG* 3.0 33.9 + - - +
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Residues in contact with GLN 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A ASP* 3.0 54.9 + - - +
674A GLY* 3.9 7.5 - - - -
675A LEU* 3.8 26.1 - - - +
573D SER* 3.0 21.8 + - - +
574D VAL 3.2 4.4 + - - +
576D ASP* 1.3 74.9 - - + +
578D LEU* 1.3 61.6 + - - +
580D ASP* 3.6 9.1 + - - +
581D LYS* 3.1 39.6 + - - +
662D VAL* 3.6 22.7 - - + +
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Residues in contact with LEU 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D VAL* 2.9 22.3 + - + +
575D LEU* 3.0 8.0 + - - +
577D GLN* 1.3 75.8 - - - +
579D GLN* 1.3 65.5 + - - +
581D LYS* 3.0 21.2 + - + +
582D ASP 3.7 2.8 + - - -
609D PHE* 4.1 18.8 - - + -
612D MET* 5.3 0.2 - - + -
627D PHE* 3.8 32.8 - - + -
631D PHE* 3.8 31.0 - - + -
655D LEU* 4.1 8.8 - - + +
659D GLY* 3.3 38.6 - - - +
662D VAL* 4.3 8.3 - - + -
663D LEU* 4.8 4.7 - - + -
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Residues in contact with GLN 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575D LEU* 2.8 20.1 + - + +
576D ASP* 3.4 6.5 + - - +
578D LEU* 1.3 76.6 - - - +
580D ASP* 1.3 57.2 + - - +
582D ASP* 2.9 30.7 + - - +
583D PRO* 4.7 0.7 - - - +
585D ARG* 3.3 41.4 + - - +
588D ALA* 4.1 8.7 + - - +
609D PHE* 3.6 48.7 - - + +
610D ALA* 5.8 0.3 - - - -
613D ARG* 2.6 31.3 + - - +
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Residues in contact with ASP 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D ASP* 3.1 24.9 + - - +
577D GLN* 3.8 11.9 - - - +
578D LEU 3.1 0.8 - - - -
579D GLN* 1.3 77.1 - - - +
581D LYS* 1.3 67.7 + - - +
582D ASP 3.2 0.8 + - - -
583D PRO* 3.7 14.3 - - - +
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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