Contacts of the helix formed by residues 669 - 687 (chain A) in PDB entry 5N6R
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 PRO 669 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A ARG* 3.8 20.6 - - - +
667A SER 4.3 3.6 - - - +
668A HIS* 1.3 96.8 - - + +
670A ASP* 1.3 59.5 + - - +
671A HIS 3.2 1.1 - - - -
672A PRO* 3.3 24.5 - - + +
673A LEU* 3.4 12.8 + - - +
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Residues in contact with ASP 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ARG* 3.6 21.3 + - - -
576A ARG* 3.5 26.2 - - - +
577A VAL 3.4 20.8 - - - +
578A GLY* 5.1 0.7 - - - -
664A THR* 3.3 23.3 + - + +
665A PRO* 5.6 0.2 - - - +
668A HIS* 3.7 22.0 + - + +
669A PRO* 1.3 77.8 - - - +
671A HIS* 1.3 64.2 + - - +
673A LEU* 3.6 9.3 + - - +
674A LEU* 3.3 31.3 + - - +
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Residues in contact with HIS 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 3.4 58.5 + - + +
662A LYS* 5.7 0.6 - - - -
664A THR* 3.7 15.7 + - + +
665A PRO 3.5 18.2 - - - +
666A ALA* 3.6 27.2 + - + +
668A HIS 3.1 5.7 + - - +
670A ASP* 1.3 75.1 - - - +
672A PRO* 1.4 76.5 - - + +
673A LEU 3.1 0.7 + - - -
674A LEU* 3.1 4.3 + - - +
675A GLN* 3.1 21.5 + - + +
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Residues in contact with PRO 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ALA 4.6 4.3 - - - +
668A HIS 3.6 7.4 - - - +
669A PRO* 3.3 20.0 - - + +
671A HIS* 1.4 99.6 - - + +
673A LEU* 1.3 53.7 + - - -
675A GLN* 3.2 10.8 + - + +
676A ASP* 2.8 31.2 + - - +
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Residues in contact with LEU 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A VAL 5.1 0.2 - - - +
578A GLY* 3.7 30.3 - - - +
579A ASP 5.1 0.7 - - - +
581A PHE* 5.5 1.8 - - + -
582A GLN* 3.3 34.9 - - + +
669A PRO 3.4 13.2 + - - +
670A ASP* 3.7 12.6 - - - +
671A HIS 3.1 0.8 + - - -
672A PRO* 1.3 76.3 - - - +
674A LEU* 1.3 83.1 + - + +
676A ASP* 3.3 8.1 + - - +
677A ALA* 3.2 24.3 + - + +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A VAL 4.4 8.3 - - - +
578A GLY* 4.7 2.5 - - - -
581A PHE* 4.8 11.2 - - + -
657A LEU* 3.9 41.9 - - + +
660A LEU* 4.0 23.8 - - + -
661A LEU* 4.2 23.3 - - + +
664A THR* 5.6 4.3 - - + +
670A ASP* 3.3 28.3 + - - +
671A HIS* 3.1 8.8 + - - +
673A LEU* 1.3 97.7 - - + +
675A GLN* 1.3 61.6 + - - +
677A ALA* 3.8 2.6 + - - -
678A LEU* 3.2 23.4 + - - +
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Residues in contact with GLN 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A HIS* 6.1 1.6 + - - -
661A LEU* 3.5 27.9 - - + +
671A HIS* 3.1 14.9 + - + +
672A PRO* 3.3 14.6 - - + +
673A LEU 3.2 0.2 - - - -
674A LEU* 1.3 76.6 - - - +
676A ASP* 1.3 57.0 + - - +
678A LEU* 3.1 17.3 + - + +
679A ARG* 2.9 60.9 + - - +
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Residues in contact with ASP 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A PRO 2.8 19.9 + - - +
673A LEU* 3.6 8.1 - - - +
675A GLN* 1.3 73.4 - - - +
677A ALA* 1.3 63.9 + - - +
679A ARG* 3.0 25.7 + - - +
680A ILE* 3.4 18.2 + - - +
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Residues in contact with ALA 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A PHE* 5.0 13.9 - - + +
582A GLN* 5.2 8.3 - - + -
585A ALA* 4.4 17.6 - - + +
657A LEU* 3.6 19.0 - - + +
673A LEU* 3.2 13.3 + - + +
674A LEU* 4.2 2.9 - - - +
676A ASP* 1.3 78.5 - - - +
678A LEU* 1.3 53.5 + - - +
680A ILE* 3.5 12.0 - - - +
681A SER* 2.8 34.3 + - - -
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Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A THR* 3.4 31.0 - - - +
657A LEU* 3.6 8.9 - - + +
658A HIS* 3.1 45.3 - - + +
661A LEU* 5.4 3.6 - - + -
674A LEU 3.2 19.0 + - - +
675A GLN* 3.1 18.7 + - - +
677A ALA* 1.3 75.5 - - - +
679A ARG* 1.3 64.6 + - - +
681A SER* 3.2 4.6 + - - +
682A GLN* 3.0 46.9 + - + +
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Residues in contact with ARG 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A GLN* 2.9 49.6 + - - +
676A ASP* 3.0 13.2 + - - +
678A LEU* 1.3 76.9 - - - +
680A ILE* 1.3 61.4 + - + +
682A GLN* 4.1 2.4 - - - +
683A ASN* 3.0 30.9 + - - +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA* 3.8 26.7 - - + +
588A LEU* 4.0 21.9 - - + +
676A ASP* 3.8 17.7 - - - +
677A ALA* 3.5 14.1 - - - +
679A ARG* 1.3 78.9 - - + +
681A SER* 1.3 67.3 + - - +
682A GLN 3.3 0.2 + - - -
683A ASN* 3.3 4.6 + - - +
684A PHE* 2.9 26.0 + - - +
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Residues in contact with SER 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA* 5.8 4.3 - - - -
588A LEU* 4.9 5.4 - - - -
654A THR* 3.7 22.9 - - - +
657A LEU* 4.2 6.5 - - - +
677A ALA 2.8 24.0 + - - -
678A LEU* 3.2 15.9 + - - +
680A ILE* 1.3 76.9 - - - +
682A GLN* 1.3 58.3 + - - +
684A PHE* 3.7 10.2 - - - +
685A LEU* 3.5 23.6 + - - +
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Residues in contact with GLN 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A THR 4.4 0.7 - - - +
652A ARG* 5.9 2.5 + - - +
654A THR* 2.7 25.6 + - - +
678A LEU* 3.0 42.0 + - + +
679A ARG* 4.1 2.2 - - - +
681A SER* 1.3 73.1 + - - +
683A ASN* 1.3 66.5 + - - +
684A PHE 3.2 0.3 + - - -
685A LEU* 3.3 20.3 + - - +
686A SER* 2.9 31.8 + - - +
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Residues in contact with ASN 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A ARG 3.0 20.0 + - - +
680A ILE* 3.3 4.5 + - - +
682A GLN* 1.3 77.1 - - - +
684A PHE* 1.3 55.8 + - - +
686A SER* 4.3 8.6 - - - -
687A SER* 2.9 51.4 + - - -
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Residues in contact with PHE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A LEU* 3.9 28.9 - - + -
591A TYR* 3.8 32.3 - + + -
592A ARG* 3.7 42.1 + - + -
595A VAL* 4.5 3.8 - - + -
650A VAL* 5.8 6.1 - - + -
651A THR* 6.1 1.8 - - + -
680A ILE 2.9 17.1 + - - +
681A SER* 3.7 11.4 - - - +
682A GLN 3.2 0.4 - - - -
683A ASN* 1.3 78.6 - - - +
685A LEU* 1.3 80.7 + - + +
687A SER* 3.4 11.8 + - - -
688A ILE* 3.6 32.5 - - + +
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A VAL 5.0 0.4 - - - +
651A THR* 3.7 44.0 - - + +
654A THR* 3.6 13.7 - - + -
681A SER 3.5 17.9 + - - +
682A GLN* 3.4 26.9 - - - +
684A PHE* 1.3 86.7 - - + +
686A SER* 1.3 86.1 + - - +
688A ILE* 2.9 24.6 + - + +
689A ASN* 3.0 13.5 + - + +
692A ILE* 4.8 4.8 - - + +
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Residues in contact with SER 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A GLN* 2.9 26.1 + - - +
683A ASN* 3.9 11.7 - - - -
685A LEU* 1.3 85.8 - - - +
687A SER* 1.3 60.7 + - - +
688A ILE 3.2 1.0 + - - -
689A ASN* 3.2 23.2 + - - +
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Residues in contact with SER 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ARG* 4.5 12.7 + - - -
683A ASN* 2.9 37.1 + - - -
684A PHE* 3.7 7.4 - - - -
685A LEU 3.2 0.6 - - - -
686A SER* 1.3 74.9 - - - +
688A ILE* 1.3 60.5 + - - +
689A ASN 3.6 0.2 - - - -
691A GLU* 4.6 4.9 - - - +
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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