Contacts of the helix formed by residues 658 - 674 (chain C) in PDB entry 3RMD
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 ARG 658 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604C TYR* 3.2 35.0 + - + +
608C VAL* 6.1 1.1 - - + -
653C LYS* 6.4 0.2 - - - +
654C PHE* 2.9 46.9 + - + +
657C GLU* 1.3 98.4 + - - +
659C MET* 1.3 62.5 + - - +
661C PRO* 3.5 5.8 - - - +
662C ALA* 3.4 14.4 + - - +
665C ARG* 5.2 0.9 + - - -
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Residues in contact with MET 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C MET* 3.7 20.2 - - - -
410C PHE* 3.5 35.7 - - + -
601C VAL* 3.8 25.4 - - + -
604C TYR* 4.2 13.7 - - + -
605C LEU* 3.7 31.4 - - + -
627C VAL* 4.3 3.6 - - + -
654C PHE* 3.2 29.6 + - + +
655C ALA* 3.0 12.7 + - - +
658C ARG* 1.3 73.7 - - - +
660C GLU* 1.3 68.0 + - - +
661C PRO 3.2 2.0 - - - -
662C ALA* 2.9 3.9 + - - +
663C ILE* 2.8 30.0 + - + +
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Residues in contact with GLU 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C PHE* 4.7 5.3 - - + -
655C ALA 2.8 21.4 + - - +
656C ARG* 3.2 23.6 - - + +
659C MET* 1.3 72.4 - - - +
661C PRO* 1.4 66.9 - - + +
663C ILE* 2.9 12.6 + - - +
664C ASP* 2.9 29.1 + - - +
683C MET 2.9 23.4 - - - +
684C ASP* 3.5 10.2 - - - +
685C ARG* 3.3 25.4 + - - +
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Residues in contact with PRO 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C ARG 3.2 11.0 - - - +
657C GLU* 3.4 17.9 - - - +
658C ARG 3.5 11.4 - - - +
659C MET 3.4 3.1 - - - -
660C GLU* 1.4 97.0 - - + +
662C ALA* 1.3 61.1 + - - +
664C ASP* 3.3 7.0 + - + +
665C ARG* 3.0 39.6 + - - +
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Residues in contact with ALA 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C ILE* 5.3 0.2 - - - +
600C LYS* 5.6 2.5 - - - +
604C TYR* 3.7 40.4 - - + -
658C ARG 3.4 11.5 + - - +
659C MET* 2.9 8.4 + - - +
661C PRO* 1.3 78.9 - - - +
663C ILE* 1.3 58.7 + - + +
665C ARG* 3.3 19.0 - - - +
666C GLY* 2.9 24.9 + - - -
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Residues in contact with ILE 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C PHE* 4.1 30.1 - - + -
597C ILE* 3.6 27.4 - - + +
600C LYS* 6.0 0.7 - - - -
601C VAL* 4.1 25.6 - - + -
659C MET* 2.8 27.8 + - + +
660C GLU* 3.2 12.3 - - - +
662C ALA* 1.3 74.5 - - + +
664C ASP* 1.3 66.9 + - - +
666C GLY* 3.0 3.8 + - - -
667C PHE* 2.9 33.2 + - + -
683C MET* 4.0 27.6 - - + +
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Residues in contact with ASP 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C GLU 2.9 14.6 + - - +
661C PRO* 3.8 9.1 - - + +
663C ILE* 1.3 73.9 - - - +
665C ARG* 1.3 64.2 + - - +
667C PHE* 3.1 6.0 + - - +
668C ARG* 3.0 53.5 + - - +
679C HIS* 3.0 26.3 + - - -
681C MET 5.3 1.5 - - - +
682C PHE* 5.5 1.6 - - - -
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Residues in contact with ARG 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C TYR* 4.6 12.9 + - - -
658C ARG 5.2 1.2 + - - -
661C PRO* 3.0 25.0 + - - +
662C ALA* 3.3 38.0 - - - +
664C ASP* 1.3 81.4 - - - +
666C GLY* 1.3 63.3 + - - +
668C ARG* 3.3 10.3 + - - +
669C GLU* 3.2 20.4 + - - +
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Residues in contact with GLY 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C TRP* 2.9 23.3 + - - -
597C ILE* 4.6 1.6 - - - -
600C LYS* 4.2 24.7 - - - -
662C ALA 2.9 15.5 + - - -
663C ILE 3.0 4.2 + - - -
665C ARG* 1.3 77.7 - - - +
667C PHE* 1.3 59.7 + - - +
669C GLU* 3.3 18.3 - - - +
670C MET 3.3 1.0 + - - -
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Residues in contact with PHE 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C LEU* 3.9 27.6 - - + -
422C GLN* 5.7 0.2 + - - -
593C ALA* 3.6 31.6 - - + -
596C TRP* 4.5 2.9 - + - -
597C ILE* 3.4 46.7 - - + -
663C ILE* 2.9 27.2 + - + +
664C ASP* 3.1 2.4 + - - +
666C GLY* 1.3 72.9 - - - +
668C ARG* 1.3 62.3 + - - +
669C GLU 3.0 1.1 - - - -
670C MET* 2.9 24.8 + - + +
671C CYS* 2.8 28.6 + - - +
679C HIS* 3.4 22.0 + - + -
681C MET* 3.6 29.8 - - + +
683C MET* 4.5 3.4 - - + -
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Residues in contact with ARG 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C ASP* 3.0 51.1 + - - +
665C ARG* 3.3 10.5 + - - +
667C PHE* 1.3 74.7 - - - +
669C GLU* 1.3 63.1 + - - +
671C CYS* 3.2 5.6 + - - +
672C GLU* 3.1 33.5 + - + +
679C HIS* 3.2 35.0 - - + +
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Residues in contact with GLU 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ALA* 5.2 4.3 - - - +
596C TRP* 3.7 14.6 - - + -
600C LYS* 3.1 33.8 + - - -
665C ARG* 3.2 9.1 + - - +
666C GLY* 3.3 12.6 - - - +
668C ARG* 1.3 80.5 - - - +
670C MET* 1.3 56.5 - - - +
672C GLU* 3.2 10.7 + - - +
673C TYR* 2.9 26.7 + - - +
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Residues in contact with MET 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLN* 4.1 4.9 - - - +
589C PHE* 3.7 31.4 - - + -
592C MET* 3.1 31.6 - - + -
593C ALA* 3.8 17.9 - - + -
596C TRP* 3.5 46.6 - - + +
666C GLY 3.3 1.6 + - - -
667C PHE* 2.9 28.6 + - + +
669C GLU* 1.3 76.7 - - - +
671C CYS* 1.3 68.1 + - - +
673C TYR* 3.2 5.1 + - + +
674C MET* 3.0 24.6 + - + +
681C MET* 3.9 10.8 - - + -
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Residues in contact with CYS 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLN* 4.0 9.4 - - - +
667C PHE 2.8 11.7 + - - +
668C ARG* 3.2 13.7 + - - +
670C MET* 1.3 77.4 - - - +
672C GLU* 1.3 55.0 + - + +
674C MET 3.4 0.9 + - - -
675C ASN 2.8 27.2 + - - -
676C ASN* 3.0 44.9 + - - +
678C GLN* 3.9 2.0 - - - -
679C HIS* 3.6 41.5 - - + +
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Residues in contact with GLU 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C ARG* 3.3 24.3 + - - +
668C ARG* 3.1 19.6 + - + +
669C GLU* 3.5 10.0 - - - +
670C MET 3.2 0.2 - - - -
671C CYS* 1.3 75.4 - - + +
673C TYR* 1.3 59.5 + - - +
675C ASN* 2.7 24.9 + - - +
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Residues in contact with TYR 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C TYR* 3.6 28.1 - + + -
445C ALA* 4.0 24.1 - - + -
447C ALA 2.5 40.2 + - - -
448C GLU 4.2 0.2 + - - -
449C ARG* 3.3 48.4 - - + +
450C PRO* 3.5 6.4 - - + +
592C MET* 5.5 1.1 - - - -
596C TRP* 4.5 14.4 - + + -
669C GLU* 2.9 14.5 + - + +
670C MET* 3.3 13.9 - - + +
672C GLU* 1.3 78.1 - - - +
674C MET* 1.3 88.8 + - + +
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Residues in contact with MET 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C PHE* 5.4 0.4 - - + -
442C TYR* 3.9 19.3 - - + -
450C PRO* 4.1 17.2 - - + +
454C TYR 3.9 0.5 - - - +
456C CYS* 3.0 46.0 + - - +
457C SER 4.1 0.4 - - - -
458C PRO* 3.6 36.8 - - + -
589C PHE* 4.7 2.5 - - + -
592C MET* 4.1 19.5 - - + -
670C MET 3.0 16.8 + - - +
673C TYR* 1.3 104.8 - - + +
675C ASN* 1.3 73.4 + - - +
676C ASN* 3.3 21.8 - - - +
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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