Contacts of the helix formed by residues 623 - 642 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H LEU* 5.5 7.2 - - - -
571H LEU* 5.1 5.2 - - - -
621H TYR* 3.3 8.0 + - - +
622H LYS* 1.3 82.7 + - - +
624H LEU* 1.3 63.3 + - - +
625H HIS* 3.0 12.3 + - - +
626H GLU* 2.9 39.3 + - - +
627H PHE* 3.6 8.7 + - - +
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Residues in contact with LEU 624 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H LEU* 5.8 1.8 - - - +
570H LEU* 5.0 2.7 - - + -
571H LEU* 4.7 17.2 - - + +
623H ASN* 1.3 75.3 - - - +
625H HIS* 1.3 57.7 + - - +
627H PHE* 3.0 9.1 + - + +
628H GLU* 2.8 56.1 + - + +
663H LEU* 4.4 15.7 - - + +
666H ALA* 3.4 42.2 - - + -
667H ARG* 3.0 31.9 - - - +
670H VAL* 4.1 20.6 - - + +
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Residues in contact with HIS 625 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623H ASN* 3.0 12.0 + - - +
624H LEU* 1.3 81.5 - - - +
626H GLU* 1.3 57.5 + - + +
628H GLU* 3.2 25.8 + - + +
629H GLU* 2.8 51.0 + - + +
632H ASP* 6.0 2.0 - - - -
667H ARG* 4.0 12.2 + - - +
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Residues in contact with GLU 626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615H ARG* 2.8 34.8 + - - +
620H GLY 3.7 0.2 - - - +
621H TYR* 3.8 12.5 - - + -
622H LYS* 3.2 56.4 + - - +
623H ASN* 2.9 25.7 + - - +
624H LEU 3.2 0.2 - - - -
625H HIS* 1.3 76.7 - - + +
627H PHE* 1.3 62.9 + - - +
629H GLU* 3.2 27.6 + - - +
630H ASP* 3.3 11.3 + - - +
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Residues in contact with PHE 627 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H LEU* 3.6 44.9 - - + -
574H VAL* 3.7 20.4 - - + -
575H LEU* 3.9 31.6 - - + -
578H LEU* 3.7 13.2 - - + -
612H MET* 3.5 25.2 - - + +
616H LEU* 4.6 6.3 - - + -
621H TYR* 3.7 36.2 - + + -
623H ASN 3.6 5.3 + - - +
624H LEU 3.0 10.2 + - - +
626H GLU* 1.3 75.8 - - - +
628H GLU* 1.3 66.0 + - - +
630H ASP* 3.1 3.3 + - - +
631H PHE* 3.0 19.8 + - + +
663H LEU* 4.1 13.0 - - + -
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Residues in contact with GLU 628 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624H LEU* 2.8 38.2 + - + +
625H HIS* 3.2 30.6 + - + +
627H PHE* 1.3 79.6 - - - +
629H GLU* 1.3 63.5 + - - +
631H PHE* 3.2 8.7 + - - +
632H ASP* 2.9 35.8 + - - +
663H LEU* 4.1 29.3 - - + +
667H ARG* 4.1 6.6 + - - +
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Residues in contact with GLU 629 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615H ARG* 6.1 0.4 - - - +
625H HIS* 2.8 40.4 + - + +
626H GLU* 3.2 28.4 + - - +
628H GLU* 1.3 72.5 - - - +
630H ASP* 1.3 65.7 + - - +
632H ASP* 3.0 21.4 + - - +
633H LEU* 3.0 16.8 + - + +
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Residues in contact with ASP 630 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607H MET* 3.4 35.6 - - + +
611H THR 5.6 0.2 - - - +
612H MET* 3.8 12.7 - - + -
615H ARG* 3.3 25.0 + - - +
621H TYR* 2.4 38.0 + - - +
626H GLU 3.3 2.4 + - - +
627H PHE 3.1 8.0 + - - +
629H GLU* 1.3 76.9 - - - +
631H PHE* 1.3 68.2 + - - +
633H LEU* 3.1 23.4 + - - +
634H ILE* 3.1 10.4 + - - +
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Residues in contact with PHE 631 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H LEU* 4.0 22.0 - - + -
609H PHE* 4.2 13.7 - + - -
612H MET* 3.8 14.6 - - + +
627H PHE* 3.0 13.3 + - + +
628H GLU* 3.2 8.3 + - - +
630H ASP* 1.3 75.0 - - - +
632H ASP* 1.3 74.4 + - - +
634H ILE* 3.0 17.9 + - + +
635H ILE* 3.2 28.1 + - + +
655H LEU* 3.3 53.8 - - + -
656H ARG* 4.5 5.8 - - + -
659H GLY* 3.8 14.8 - - - -
660H GLY* 4.5 2.9 - - - -
663H LEU* 3.4 30.7 - - + -
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Residues in contact with ASP 632 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625H HIS* 6.0 2.3 - - - -
628H GLU* 2.9 30.0 + - - +
629H GLU* 3.2 14.1 - - - +
631H PHE* 1.3 89.1 - - - +
633H LEU* 1.3 54.9 + - - +
635H ILE* 3.1 7.3 + - - +
636H ASP* 2.8 48.1 + - - +
656H ARG* 6.1 1.0 - - - +
663H LEU* 5.6 0.3 - - - +
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Residues in contact with LEU 633 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605H HIS* 3.7 40.6 - - + +
607H MET* 3.6 20.9 - - + -
629H GLU* 3.0 14.8 + - + +
630H ASP* 3.1 25.5 + - - +
632H ASP* 1.3 72.7 - - - +
634H ILE* 1.3 68.7 + - - +
636H ASP* 4.5 4.3 - - + +
637H ASN* 2.9 42.7 + - - +
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Residues in contact with ILE 634 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587H PHE* 3.3 37.2 - - + +
607H MET* 3.7 29.1 - - + +
608H ASP* 3.7 13.2 - - - +
609H PHE* 3.6 36.6 - - + +
612H MET* 3.6 18.6 - - - -
630H ASP 3.1 7.4 + - - +
631H PHE* 3.0 11.0 + - + +
633H LEU* 1.3 79.9 - - - +
635H ILE* 1.3 64.2 + - + +
637H ASN* 4.0 2.6 - - - +
638H CYS* 3.3 21.1 + - - +
655H LEU* 4.6 9.2 - - + -
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Residues in contact with ILE 635 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587H PHE* 5.7 0.4 - - + -
631H PHE* 3.6 28.9 - - + +
632H ASP* 3.1 9.5 + - - +
634H ILE* 1.3 80.8 - - + +
636H ASP* 1.3 64.8 + - - +
638H CYS* 4.1 1.9 - - - +
639H MET* 3.2 49.6 + - - +
652H ALA* 3.6 25.4 - - - +
655H LEU* 3.8 25.4 - - + -
656H ARG* 3.7 39.3 - - + +
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Residues in contact with ASP 636 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632H ASP* 2.8 37.0 + - - +
633H LEU* 4.3 5.3 - - + +
635H ILE* 1.3 81.8 - - - +
637H ASN* 1.3 56.6 + - - +
639H MET* 3.3 15.4 + - + +
640H LYS* 2.7 38.9 + - - +
656H ARG* 5.7 1.4 - - - -
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Residues in contact with ASN 637 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599H TYR* 3.5 16.3 + - - +
603H ILE* 3.5 34.6 - - + +
604H LYS 5.1 0.5 + - - -
605H HIS 2.7 29.4 + - - +
606H PRO* 3.4 14.8 - - - +
607H MET 3.6 8.8 + - - +
633H LEU* 2.9 33.1 + - - +
634H ILE* 4.0 2.7 - - - +
636H ASP* 1.3 77.4 - - - +
638H CYS* 1.3 63.8 + - - +
640H LYS 3.1 1.2 + - - -
641H TYR* 3.0 23.2 + - - +
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Residues in contact with CYS 638 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587H PHE* 3.7 23.8 - - + -
599H TYR* 4.4 4.9 + - - +
634H ILE 3.3 16.7 + - - +
635H ILE 4.1 2.5 - - - +
637H ASN* 1.3 79.4 - - - +
639H MET* 1.3 56.1 + - - +
641H TYR* 4.9 0.4 - - - -
642H ASN* 3.1 43.4 + - - +
648H PHE* 3.6 32.3 - - - -
649H TYR* 5.2 0.7 + - - -
652H ALA* 3.6 22.0 - - + -
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Residues in contact with MET 639 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635H ILE* 3.2 35.0 + - + +
636H ASP* 3.7 18.8 - - - +
638H CYS* 1.3 75.2 - - - +
640H LYS* 1.3 64.4 + - - +
642H ASN 4.1 4.5 - - - +
649H TYR* 3.6 56.0 - - + +
652H ALA* 3.8 15.9 - - + -
653H VAL* 4.4 11.2 - - - -
656H ARG* 4.4 22.0 - - - +
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Residues in contact with LYS 640 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602H HIS* 5.0 7.2 - - + +
603H ILE* 4.0 14.8 - - + -
636H ASP 2.7 21.5 + - - +
637H ASN 3.8 3.1 - - - +
639H MET* 1.3 74.0 - - - +
641H TYR* 1.3 64.7 + - - +
642H ASN 4.4 1.2 - - - +
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Residues in contact with TYR 641 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B VAL* 4.0 12.6 - - - +
650B ARG* 5.2 2.3 + - - -
596H VAL* 2.9 25.8 - - + +
598H ASP* 2.7 40.7 + - - -
599H TYR* 3.6 30.3 - + + -
602H HIS* 3.8 30.1 - + + -
603H ILE* 4.6 3.8 - - + +
637H ASN 3.0 15.5 + - - +
640H LYS* 1.3 81.0 - - - +
642H ASN* 1.3 91.8 + - - +
643H ALA* 4.0 0.5 + - - -
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Residues in contact with ASN 642 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599H TYR* 5.5 2.1 - - - -
638H CYS* 3.1 36.8 + - - +
639H MET 4.1 11.4 - - - +
640H LYS 4.4 1.0 - - - +
641H TYR* 1.3 106.0 - - - +
643H ALA* 1.3 65.4 + - - +
644H ARG 3.9 0.5 + - - -
646H THR* 4.8 3.6 - - - -
648H PHE* 3.5 42.4 - - + -
649H TYR* 4.4 7.0 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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