Contacts of the helix formed by residues 623 - 642 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G EDO 3.1 33.3 - - - +
567G LEU* 4.3 13.5 - - - -
621G TYR* 3.3 6.2 - - - +
622G LYS* 1.3 91.1 + - - +
624G LEU* 1.3 67.3 + - - +
625G HIS* 3.2 9.9 + - - +
626G GLU* 2.9 51.4 + - - +
627G PHE* 3.5 9.7 + - - +
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Residues in contact with LEU 624 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G EDO 3.0 11.7 + - - +
567G LEU* 4.7 3.0 - - + +
570G LEU* 5.3 0.9 - - + -
571G LEU* 3.6 27.8 - - + -
574G VAL* 5.2 0.7 - - + -
623G ASN* 1.3 71.3 - - - +
625G HIS* 1.3 69.7 + - - +
627G PHE* 3.0 8.8 + - + +
628G GLU* 2.9 42.9 + - - +
663G LEU* 4.1 17.3 - - + +
666G ALA* 3.7 20.6 - - + +
667G ARG* 3.5 53.8 - - + +
670G VAL* 4.3 10.3 - - + -
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Residues in contact with HIS 625 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G EDO 3.2 14.2 + - - +
623G ASN* 3.2 11.0 - - - +
624G LEU* 1.3 79.6 - - - +
626G GLU* 1.3 63.6 + - + +
628G GLU* 3.2 20.6 + - + +
629G GLU* 3.0 60.3 + - + +
667G ARG* 4.0 4.7 + - - +
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Residues in contact with GLU 626 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615G ARG* 3.4 29.0 + - - +
620G GLY 3.7 2.3 - - - +
621G TYR* 3.7 12.8 - - + -
622G LYS* 2.9 45.9 + - - +
623G ASN* 2.9 27.4 + - - +
624G LEU 3.1 0.8 - - - -
625G HIS* 1.3 80.8 - - + +
627G PHE* 1.3 60.8 + - - +
629G GLU* 3.4 14.6 + - - +
630G ASP* 3.3 17.7 + - - +
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Residues in contact with PHE 627 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 3.7 42.2 - - + -
574G VAL* 3.5 22.0 - - + -
575G LEU* 3.7 38.8 - - + -
578G LEU* 3.7 14.4 - - + -
612G MET* 3.6 25.3 - - + +
616G LEU* 4.8 1.8 - - + -
621G TYR* 3.4 41.4 - + + -
623G ASN 3.5 4.4 + - - +
624G LEU* 3.0 9.6 + - + +
626G GLU* 1.3 77.6 - - - +
628G GLU* 1.3 58.1 + - - +
630G ASP* 3.0 8.1 + - - +
631G PHE* 3.0 23.3 + - + +
663G LEU* 4.1 12.8 - - + -
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Residues in contact with GLU 628 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624G LEU* 2.9 36.8 + - + +
625G HIS* 3.5 23.5 + - + +
627G PHE* 1.3 75.6 - - - +
629G GLU* 1.3 60.7 + - - +
631G PHE* 3.3 7.6 + - - +
632G ASP* 2.8 41.8 + - - +
663G LEU* 4.0 36.3 - - + +
667G ARG* 4.0 11.4 + - - +
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Residues in contact with GLU 629 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625G HIS* 3.0 52.6 + - + +
626G GLU* 3.8 13.6 - - - +
627G PHE 3.3 0.2 - - - -
628G GLU* 1.3 75.2 - - - +
630G ASP* 1.3 64.4 + - - +
632G ASP* 3.4 9.0 + - - +
633G LEU* 2.9 26.7 + - - +
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Residues in contact with ASP 630 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607G MET* 3.5 36.2 - - + +
612G MET* 3.8 12.5 - - + -
615G ARG* 3.3 31.0 + - - +
621G TYR* 2.6 30.4 + - - +
626G GLU 3.3 5.2 + - - +
627G PHE 3.0 11.4 + - - +
629G GLU* 1.3 77.0 - - - +
631G PHE* 1.3 63.6 + - - +
633G LEU* 3.0 22.8 + - - +
634G ILE* 3.1 9.4 + - - +
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Residues in contact with PHE 631 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578G LEU* 3.6 30.5 - - + -
609G PHE* 4.1 15.9 - + - -
612G MET* 3.8 12.9 - - + -
627G PHE* 3.0 13.5 + - + +
628G GLU* 3.3 9.8 + - - +
630G ASP* 1.3 76.1 - - - +
632G ASP* 1.3 68.8 + - - +
634G ILE* 3.0 28.8 + - + +
635G ILE* 3.4 18.3 + - + +
655G LEU* 3.5 46.2 - - + -
656G ARG* 4.5 7.2 - - + -
659G GLY* 3.8 14.1 - - - -
660G GLY* 4.6 1.8 - - - -
663G LEU* 3.7 26.7 - - + -
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Residues in contact with ASP 632 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628G GLU* 2.8 31.8 + - - +
629G GLU* 3.8 8.8 - - - +
631G PHE* 1.3 83.4 - - - +
633G LEU* 1.3 60.6 + - - +
635G ILE* 3.4 6.5 + - - +
636G ASP* 2.9 49.0 + - - +
656G ARG* 6.0 1.6 - - - +
663G LEU* 5.3 1.6 - - - +
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Residues in contact with LEU 633 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605G HIS* 3.3 42.8 - - + +
607G MET* 3.9 17.7 - - + -
629G GLU 2.9 13.2 + - - +
630G ASP* 3.1 27.4 - - - +
632G ASP* 1.3 74.1 - - - +
634G ILE* 1.3 67.1 + - - +
636G ASP* 4.6 4.9 - - + -
637G ASN* 2.9 47.0 + - - +
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Residues in contact with ILE 634 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587G PHE* 3.7 35.6 - - + +
607G MET* 3.8 20.9 - - + +
608G ASP* 3.7 31.6 - - - +
609G PHE* 3.8 20.6 - - + +
612G MET* 3.8 22.2 - - - -
630G ASP 3.1 7.8 + - - +
631G PHE* 3.0 12.8 + - + +
633G LEU* 1.3 81.6 - - - +
635G ILE* 1.3 70.2 + - + +
637G ASN* 3.9 3.0 - - - +
638G CYS* 3.3 20.8 + - - +
655G LEU* 4.4 4.0 - - + -
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Residues in contact with ILE 635 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587G PHE* 5.6 0.7 - - + -
631G PHE* 3.8 26.7 - - + +
632G ASP* 3.4 8.7 + - - +
633G LEU 3.2 0.2 - - - -
634G ILE* 1.3 81.4 - - + +
636G ASP* 1.3 64.4 + - - +
638G CYS* 3.3 2.3 + - - +
639G MET* 2.9 53.4 + - + +
652G ALA* 3.6 33.2 - - + +
655G LEU* 3.8 28.9 - - + -
656G ARG* 3.8 26.7 - - + +
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Residues in contact with ASP 636 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632G ASP* 2.9 33.8 + - - +
633G LEU* 4.2 5.1 - - + +
635G ILE* 1.3 85.6 - - - +
637G ASN* 1.3 59.6 + - - +
639G MET* 3.4 7.1 + - - +
640G LYS* 2.8 41.1 + - + +
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Residues in contact with ASN 637 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599G TYR* 3.4 16.9 + - - +
603G ILE* 3.4 30.9 - - + +
604G LYS 5.5 0.2 + - - -
605G HIS 2.8 27.6 + - - +
606G PRO* 3.7 6.7 - - - +
607G MET 3.9 8.0 + - - +
633G LEU* 2.9 36.8 + - - +
634G ILE* 3.9 3.6 - - - +
636G ASP* 1.3 78.7 - - - +
638G CYS* 1.3 57.5 + - - +
640G LYS* 3.3 1.5 + - - +
641G TYR* 2.9 33.8 + - - +
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Residues in contact with CYS 638 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586G ILE* 5.5 0.4 - - - -
587G PHE* 3.7 23.3 - - + -
599G TYR* 4.8 2.7 + - - -
634G ILE 3.3 15.0 + - - +
635G ILE 3.7 3.6 - - - +
636G ASP 3.3 0.4 - - - -
637G ASN* 1.3 80.0 - - - +
639G MET* 1.3 58.7 + - - +
641G TYR* 5.0 0.2 - - - -
642G ASN* 2.9 57.6 + - - +
648G PHE* 3.5 32.8 - - - -
652G ALA* 3.8 9.9 - - + -
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Residues in contact with MET 639 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635G ILE* 2.9 39.8 + - - +
636G ASP* 4.1 7.6 - - - +
638G CYS* 1.3 73.9 - - - +
640G LYS* 1.3 60.3 + - + +
642G ASN 3.7 9.8 - - - +
649G TYR* 3.3 53.3 - - + +
652G ALA* 3.9 14.8 - - + -
653G VAL* 3.7 19.7 - - + -
656G ARG* 4.1 19.7 - - - +
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Residues in contact with LYS 640 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602G HIS* 6.0 1.0 - - - -
603G ILE* 4.4 11.9 - - + -
636G ASP* 2.8 29.0 + - + +
637G ASN 3.8 3.6 - - - +
638G CYS 3.2 0.2 - - - -
639G MET* 1.3 75.9 - - + +
641G TYR* 1.3 64.2 + - - +
642G ASN 3.7 1.6 + - - +
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Residues in contact with TYR 641 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596G VAL* 3.3 22.2 - - + +
598G ASP* 2.7 40.6 + - - -
599G TYR* 4.0 32.3 - + + -
602G HIS* 4.0 33.7 - + + -
603G ILE* 4.3 6.3 - - + -
637G ASN 2.9 17.0 + - - +
640G LYS* 1.3 79.8 - - - +
642G ASN* 1.3 81.6 + - - +
643G ALA 4.0 1.2 + - - -
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Residues in contact with ASN 642 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599G TYR* 5.8 1.4 - - - -
638G CYS* 2.9 46.3 + - - +
639G MET 3.7 8.0 - - - +
640G LYS 4.5 1.6 - - - +
641G TYR* 1.3 99.7 - - - +
643G ALA* 1.3 64.2 + - - +
646G THR* 3.6 19.8 + - + +
648G PHE* 3.8 26.7 - - - +
649G TYR* 3.4 21.6 - - - +
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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
------------------------------------------------------------
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