Contacts of the helix formed by residues 669 - 684 (chain C) in PDB entry 1DE4
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 PHE 669 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C ASP* 2.7 16.1 + - - +
668C ARG* 1.3 76.0 - - + +
670C VAL* 1.3 67.8 + - + +
671C MET 3.1 1.6 - - - -
672C LYS* 3.0 17.7 + - + +
673C LYS* 3.2 16.4 + - + +
397F VAL* 3.9 21.3 - - + -
398F GLU* 4.4 14.4 - - + -
668F ARG* 3.5 65.3 - - + +
669F PHE* 4.0 19.1 - + + -
672F LYS* 4.2 31.6 - - + -
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Residues in contact with VAL 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C ALA* 4.7 15.7 - - + -
664C GLU* 3.4 17.5 - - - +
667C ASP* 3.1 35.9 + - + +
669C PHE* 1.3 84.1 - - + +
671C MET* 1.3 70.0 + - + +
673C LYS* 3.5 12.9 + - + +
674C LEU* 3.3 27.7 + - + +
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Residues in contact with MET 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C VAL* 3.8 27.8 - - + +
606C GLU* 3.7 30.3 - - + -
660C PHE* 4.4 10.8 - - + -
663C ALA* 4.3 18.2 - - - -
664C GLU 3.9 11.0 - - - +
665C LYS* 3.9 32.5 - - + +
667C ASP 3.1 15.0 + - - +
668C ARG* 4.4 8.1 - - - +
669C PHE 3.1 0.8 - - - -
670C VAL* 1.3 82.0 - - + +
672C LYS* 1.3 63.2 + - - +
674C LEU* 3.5 10.4 + - - +
675C ASN* 2.9 34.5 + - - +
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Residues in contact with LYS 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLU* 2.9 36.3 - - - +
400C ASP* 4.7 9.3 + - - -
401C HIS* 3.4 27.5 + - + -
477C LYS* 5.2 1.8 - - - +
668C ARG 3.4 14.8 + - - +
669C PHE* 3.0 14.5 + - + +
671C MET* 1.3 79.0 - - - +
673C LYS* 1.3 63.9 + - - +
675C ASN* 3.1 8.1 + - + +
676C ASP* 2.9 45.7 + - - +
669F PHE* 4.2 20.9 - - + -
672F LYS* 5.8 10.6 - - + +
676F ASP* 4.6 12.9 + - - -
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Residues in contact with LYS 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C PHE* 3.2 12.7 + - + +
670C VAL* 3.6 16.8 - - + +
671C MET 3.3 0.2 - - - -
672C LYS* 1.3 80.0 - - - +
674C LEU* 1.3 65.1 + - + +
676C ASP* 3.3 21.2 + - - +
677C ARG* 3.4 26.6 - - + +
752C ASP* 4.6 10.4 + - - -
399F PRO* 4.1 16.6 - - - +
400F ASP* 3.6 47.2 + - - +
477F LYS* 5.8 2.0 - - - +
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Residues in contact with LEU 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C LEU* 4.2 6.4 - - + +
659C ASP* 3.7 40.8 - - + +
660C PHE* 3.8 38.5 - - + +
663C ALA* 4.1 12.6 - - + -
670C VAL* 3.3 22.0 + - + +
671C MET* 4.0 7.0 - - - +
672C LYS 3.3 0.4 - - - -
673C LYS* 1.3 76.5 - - + +
675C ASN* 1.3 66.5 + - - +
677C ARG* 3.1 41.8 + - - +
678C VAL* 3.3 13.7 + - - +
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Residues in contact with ASN 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLU* 5.2 6.2 + - - +
446C ARG* 4.7 2.8 - - - +
605C VAL 2.9 24.8 + - - +
606C GLU* 4.6 0.2 - - - +
607C LEU* 3.4 37.7 + - + +
660C PHE* 3.8 18.1 - - - -
671C MET* 2.9 31.2 + - - +
672C LYS* 3.7 7.5 - - + +
674C LEU* 1.3 73.4 - - - +
676C ASP* 1.3 65.3 + - - +
677C ARG 3.3 0.2 - - - -
678C VAL* 3.1 9.3 + - - +
679C MET* 3.0 35.5 + - + +
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Residues in contact with ASP 676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C HIS* 3.9 11.4 - - - -
672C LYS* 2.9 51.9 + - - +
673C LYS* 3.4 12.7 - - - +
674C LEU 3.1 0.4 - - - -
675C ASN* 1.3 74.7 - - - +
677C ARG* 1.3 67.5 + - + +
679C MET* 3.1 18.0 + - - +
680C ARG* 3.2 25.1 + - - +
477F LYS* 5.1 13.7 + - - +
672F LYS* 4.7 12.0 + - - -
676F ASP* 5.6 0.7 - - - +
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Residues in contact with ARG 677 (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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655C ARG* 4.4 2.2 - - - +
656C LEU* 3.3 31.7 - - + +
659C ASP* 3.3 21.4 + - - -
673C LYS* 3.4 28.1 + - + +
674C LEU* 3.1 32.8 + - - +
676C ASP* 1.3 78.4 - - + +
678C VAL* 1.3 61.9 + - - +
680C ARG* 3.4 14.6 + - - +
681C VAL* 3.4 17.3 + - - +
748C ALA 4.5 6.1 - - - +
749C LEU* 3.2 31.5 + - + +
750C SER 3.9 10.7 + - - -
751C GLY* 3.9 19.5 - - - -
477F LYS* 6.6 0.2 - - - +
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Residues in contact with VAL 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C LEU* 5.2 3.7 - - + +
607C LEU* 4.0 14.4 - - + +
609C LEU* 3.8 39.9 - - + +
611C TYR* 4.1 10.5 - - + -
656C LEU* 4.0 12.6 - - + -
660C PHE* 3.9 26.9 - - + -
674C LEU 3.5 13.5 - - - +
675C ASN* 3.3 12.1 - - - +
676C ASP 3.1 0.6 - - - -
677C ARG* 1.3 75.4 - - - +
679C MET* 1.3 65.9 + - - +
681C VAL* 3.1 25.7 + - + +
682C GLU 4.5 0.7 + - - -
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Residues in contact with MET 679 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLU* 5.2 1.8 - - - +
401C HIS* 3.2 43.5 - - + +
446C ARG* 5.9 0.7 - - - +
476C LEU* 4.0 33.7 - - + +
477C LYS 5.0 0.2 - - - +
479C PHE* 3.9 31.0 - - + -
549C GLY 5.2 1.4 - - - +
551C PRO* 5.7 1.7 - - - +
607C LEU* 3.8 26.0 - - + -
609C LEU* 5.1 5.2 - - + -
672C LYS* 5.8 0.2 - - + -
675C ASN* 3.0 32.0 + - + +
676C ASP* 3.1 12.7 + - - +
678C VAL* 1.3 76.9 - - - +
680C ARG* 1.3 61.6 + - + +
681C VAL 3.5 0.5 + - - -
682C GLU* 4.2 8.7 + - - +
683C TYR* 4.3 4.2 + - - +
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Residues in contact with ARG 680 (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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476C LEU* 3.9 30.2 - - + +
676C ASP* 3.2 19.5 + - - +
677C ARG* 3.7 12.1 - - - +
678C VAL 3.1 0.8 - - - -
679C MET* 1.3 77.8 - - + +
681C VAL* 1.3 62.9 + - - +
682C GLU 3.5 0.7 - - - -
683C TYR* 3.4 4.1 + - + +
684C HIS* 2.9 50.0 + - + +
472F SER 3.8 19.4 + - - -
473F SER 5.3 0.2 + - - -
475F HIS* 2.8 42.5 + - - +
476F LEU* 3.5 20.0 + - - +
477F LYS* 3.8 29.1 - - - +
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Residues in contact with VAL 681 (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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501C LEU* 4.3 13.5 - - + -
611C TYR* 4.1 24.9 - - + -
614C TYR* 4.5 10.8 - - + -
649C PHE* 4.4 20.0 - - + -
677C ARG 3.4 12.8 - - - +
678C VAL* 3.1 20.7 + - - +
680C ARG* 1.3 79.8 - - - +
682C GLU* 1.3 64.1 + - - +
684C HIS* 3.3 13.3 + - - +
685C PHE* 3.8 15.4 + - + -
745C ALA* 5.6 0.7 - - + +
749C LEU* 3.6 24.5 - - + -
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Residues in contact with GLU 682 (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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499C SER* 2.5 33.9 + - - -
501C LEU* 3.4 12.1 - - + +
545C LEU* 3.3 17.1 - - + +
549C GLY* 3.3 26.6 - - - +
551C PRO* 3.4 25.6 - - + +
614C TYR* 2.6 27.6 + - - -
678C VAL 4.5 0.4 + - - -
679C MET 4.2 5.2 + - - +
680C ARG 3.5 0.4 - - - -
681C VAL* 1.3 79.9 - - - +
683C TYR* 1.3 62.9 + - - +
685C PHE* 3.3 17.5 + - - +
686C LEU* 4.1 2.9 + - - +
699C HIS* 3.0 18.3 + - + -
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Residues in contact with TYR 683 (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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475C HIS* 3.4 34.9 - + - -
476C LEU* 4.2 18.8 - - + -
548C SER 5.2 4.5 - - - +
549C GLY* 3.9 9.3 + - - +
679C MET 4.3 2.4 + - - +
680C ARG* 3.4 10.2 + - + +
681C VAL 3.2 0.2 - - - -
682C GLU* 1.3 81.2 - - - +
684C HIS* 1.3 81.6 + + - +
685C PHE 3.0 4.9 + - - -
686C LEU* 3.0 45.1 + - + +
698C ARG* 4.9 8.3 - - - -
475F HIS* 4.0 22.8 + + + -
683F TYR* 3.9 16.3 + - - -
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Residues in contact with HIS 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C ARG* 2.9 53.2 + - + +
681C VAL* 3.3 8.6 + - - +
683C TYR* 1.3 96.9 - + - +
685C PHE* 1.3 60.9 + - - +
686C LEU 3.3 6.6 + - - +
688C PRO* 5.4 1.2 - - - +
741C THR* 3.8 20.1 - - - +
745C ALA* 4.2 20.7 + - + +
748C ALA* 3.8 18.4 - - + +
749C LEU* 5.6 0.9 - - - -
472F SER* 3.3 44.6 + - - -
475F HIS* 5.3 2.0 - - + -
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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
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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