Contacts of the helix formed by residues 623 - 642 (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 ASN 623 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D LEU* 3.4 16.2 - - - -
571D LEU* 5.0 0.9 - - - -
621D TYR* 3.3 4.5 - - - +
622D LYS* 1.3 82.3 + - - +
624D LEU* 1.3 64.0 + - - +
625D HIS* 3.0 23.1 + - - +
626D GLU* 3.0 45.8 + - - +
627D PHE* 3.4 10.2 + - - +
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Residues in contact with LEU 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D LEU* 4.1 8.4 - - + +
570D LEU* 5.4 0.9 - - + -
571D LEU* 3.5 27.6 - - + -
623D ASN* 1.3 75.6 - - - +
625D HIS* 1.3 58.0 + - - +
627D PHE* 3.2 5.6 + - + +
628D GLU* 2.9 36.0 + - - +
663D LEU* 4.1 25.8 - - + +
666D ALA* 3.6 19.5 - - + +
667D ARG* 3.5 53.2 - - - +
670D VAL* 3.9 17.9 - - + -
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Residues in contact with HIS 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623D ASN* 3.0 12.2 + - - +
624D LEU* 1.3 79.9 - - - +
626D GLU* 1.3 60.4 + - + +
628D GLU* 3.2 26.3 + - + +
629D GLU* 2.9 62.9 + - + +
667D ARG* 4.1 11.2 + - - +
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Residues in contact with GLU 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ACT 3.2 48.9 - - + +
615D ARG* 3.9 6.2 + - - -
621D TYR* 3.7 15.7 - - + -
622D LYS* 2.8 50.3 + - - +
623D ASN* 3.0 35.6 + - - +
625D HIS* 1.3 79.1 - - + +
627D PHE* 1.3 63.2 + - - +
629D GLU* 3.3 8.9 + - - +
630D ASP* 3.3 4.7 + - - +
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Residues in contact with PHE 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D LEU* 3.7 46.7 - - + -
574D VAL* 3.8 26.7 - - + -
575D LEU* 4.0 27.6 - - + -
578D LEU* 3.8 11.9 - - + -
612D MET* 3.5 27.1 - - + +
616D LEU* 4.7 5.6 - - + -
621D TYR* 3.4 28.3 - + + -
623D ASN 3.4 5.8 + - - +
624D LEU* 3.2 8.5 + - + +
626D GLU* 1.3 76.4 - - - +
628D GLU* 1.3 67.3 + - - +
630D ASP* 3.0 15.2 + - - +
631D PHE* 3.2 9.7 + - + -
663D LEU* 4.0 15.0 - - + -
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Residues in contact with GLU 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D LEU* 2.9 26.7 + - + +
625D HIS* 3.2 29.6 + - + +
627D PHE* 1.3 79.6 - - - +
629D GLU* 1.3 58.6 + - + +
631D PHE* 3.2 7.2 + - - +
632D ASP* 2.9 40.6 + - - +
663D LEU* 3.9 36.8 - - + +
667D ARG* 3.8 19.3 + - - +
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Residues in contact with GLU 629 (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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1D ACT 2.9 37.0 - - - +
625D HIS* 2.9 54.7 + - + +
626D GLU* 3.4 2.2 - - - +
627D PHE 3.1 0.2 - - - -
628D GLU* 1.3 75.3 - - - +
630D ASP* 1.3 65.4 + - - +
632D ASP* 3.6 8.8 + - - +
633D LEU* 3.2 21.9 + - - +
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Residues in contact with ASP 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ACT 4.1 6.1 - - - +
607D MET* 3.6 28.3 - - + +
612D MET* 3.6 19.1 - - + +
615D ARG* 3.1 29.5 + - - -
621D TYR* 2.6 25.2 + - - +
626D GLU 3.3 1.9 + - - -
627D PHE 3.0 9.8 + - - +
629D GLU* 1.3 77.8 - - - +
631D PHE* 1.3 66.2 + - - +
633D LEU* 3.0 24.3 + - - +
634D ILE* 3.0 15.4 + - - +
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Residues in contact with PHE 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D LEU* 3.8 27.6 - - + -
609D PHE* 4.1 15.3 - + - -
612D MET* 3.9 13.2 - - + -
627D PHE* 3.2 9.5 + - + +
628D GLU* 3.2 10.7 + - - +
630D ASP* 1.3 79.7 - - - +
632D ASP* 1.3 72.5 + - - +
634D ILE* 3.0 17.8 + - + +
635D ILE* 3.1 33.4 + - + +
655D LEU* 3.4 46.0 - - + -
656D ARG* 4.4 7.9 - - + -
659D GLY* 4.0 11.9 - - - -
660D GLY* 4.7 0.7 - - - -
663D LEU* 3.7 25.8 - - + -
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Residues in contact with ASP 632 (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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628D GLU* 2.9 29.8 + - - +
629D GLU* 3.9 8.9 - - - +
630D ASP 3.2 0.2 - - - -
631D PHE* 1.3 83.1 - - - +
633D LEU* 1.3 55.8 + - - +
635D ILE* 3.0 8.8 + - - +
636D ASP* 2.7 50.7 + - - +
656D ARG* 5.8 3.3 - - - +
663D LEU* 5.8 0.5 - - - +
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Residues in contact with LEU 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D HIS* 3.3 44.4 - - + +
607D MET* 4.0 19.1 - - + -
629D GLU 3.2 10.2 + - - +
630D ASP* 3.0 27.7 + - - +
632D ASP* 1.3 78.4 - - - +
634D ILE* 1.3 54.5 + - - +
636D ASP* 4.5 5.6 - - + +
637D ASN* 2.8 51.1 + - - +
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Residues in contact with ILE 634 (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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587D PHE* 3.4 38.1 - - + -
607D MET* 3.5 35.9 - - + +
608D ASP 3.6 19.5 - - - +
609D PHE* 3.8 18.2 - - + +
612D MET* 3.5 31.4 - - - -
630D ASP 3.0 8.8 + - - +
631D PHE* 3.0 8.9 + - + +
633D LEU* 1.3 76.8 - - - +
635D ILE* 1.3 73.5 + - + +
637D ASN* 4.1 3.1 - - - +
638D CYS* 3.3 17.5 + - - +
655D LEU* 4.9 3.6 - - + -
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Residues in contact with ILE 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D PHE* 5.5 0.4 - - + -
631D PHE* 3.1 32.5 + - + +
632D ASP* 3.0 9.9 + - - +
634D ILE* 1.3 82.8 - - + +
636D ASP* 1.3 61.4 + - - +
638D CYS* 3.1 3.5 + - - +
639D MET* 2.9 50.8 + - + +
652D ALA* 3.6 34.3 - - + +
655D LEU* 3.8 28.0 - - + -
656D ARG* 3.8 26.2 - - + +
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Residues in contact with ASP 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ASP* 2.7 33.7 + - - +
633D LEU* 4.1 5.3 - - + +
635D ILE* 1.3 72.4 - - - +
637D ASN* 1.3 69.5 + - - +
639D MET* 3.0 27.2 + - - +
640D LYS* 2.8 27.4 + - - +
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Residues in contact with ASN 637 (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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599D TYR* 3.4 18.1 + - - +
603D ILE* 3.3 33.0 - - + +
605D HIS 2.8 24.6 + - - +
606D PRO* 3.3 16.4 - - - +
607D MET 3.3 11.0 + - - +
633D LEU* 2.8 39.9 + - - +
634D ILE* 4.1 3.1 - - - +
636D ASP* 1.3 70.9 - - - +
638D CYS* 1.3 57.5 + - - +
641D TYR* 2.8 28.9 + - - +
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Residues in contact with CYS 638 (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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586D ILE* 5.6 0.2 - - - -
587D PHE* 3.7 22.0 - - + -
599D TYR* 5.4 1.8 - - - -
634D ILE 3.3 10.8 + - - +
635D ILE 3.1 9.1 + - - +
636D ASP 3.1 0.6 - - - -
637D ASN* 1.3 80.4 - - - +
639D MET* 1.3 61.9 + - - +
641D TYR* 4.9 0.9 - - - -
642D ASN* 3.0 47.5 + - - +
648D PHE* 3.3 33.2 - - - -
649D TYR* 5.0 0.7 - - - -
652D ALA* 3.7 10.1 - - + -
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Residues in contact with MET 639 (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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635D ILE* 2.9 34.8 + - + +
636D ASP* 3.0 28.7 + - - +
638D CYS* 1.3 76.2 - - - +
640D LYS* 1.3 59.2 + - - +
642D ASN 3.5 12.1 - - - +
649D TYR* 3.7 36.0 - - + +
652D ALA* 4.1 11.9 - - + -
653D VAL* 4.1 22.0 - - + -
656D ARG* 4.9 12.1 - - - -
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Residues in contact with LYS 640 (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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602D HIS* 2.7 37.9 + - + +
603D ILE* 3.8 14.2 - - + +
604D LYS* 5.4 1.2 - - - +
636D ASP 2.8 15.8 + - - +
637D ASN 3.6 3.1 - - - +
639D MET* 1.3 78.5 - - - +
641D TYR* 1.3 67.9 + - - +
642D ASN 3.4 1.6 + - - +
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Residues in contact with TYR 641 (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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596D VAL* 3.0 22.6 - - + +
598D ASP* 2.6 29.8 + - - -
599D TYR* 3.7 36.1 - + + -
602D HIS* 3.8 37.3 - + + -
603D ILE* 4.2 2.2 - - + +
637D ASN 2.8 20.3 + - - +
638D CYS* 4.9 0.7 - - - -
640D LYS* 1.3 76.1 - - - +
642D ASN* 1.3 87.7 + - - +
643D ALA 4.1 0.7 + - - -
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Residues in contact with ASN 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D CYS* 3.0 43.6 + - - +
639D MET 3.5 15.8 - - - +
640D LYS 4.4 1.5 - - - +
641D TYR* 1.3 102.9 - - - +
643D ALA* 1.3 65.2 + - - +
646D THR* 3.5 19.3 - - + +
648D PHE* 3.8 23.8 - - - +
649D TYR* 3.6 10.4 - - + +
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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
------------------------------------------------------------
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