Contacts of the helix formed by residues 670 - 687 (chain S) in PDB entry 5IJ7
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 SER 670 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 4.9 3.8 - - - +
633S ASN* 3.0 15.3 + - - -
664S HIS* 4.1 2.5 - - - -
669S ILE* 1.4 79.7 - - - +
671S ILE* 1.3 69.5 + - - +
672S MET* 3.7 26.9 - - - +
673S SER* 3.2 35.9 + - - -
674S ILE* 3.6 6.1 + - - +
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Residues in contact with ILE 671 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 4.7 7.4 - - - +
446A THR* 4.7 10.5 - - + +
447A TYR* 3.5 36.7 + - + +
664S HIS* 3.5 27.6 + - + -
670S SER* 1.3 76.4 - - - +
672S MET* 1.4 74.3 + - + +
674S ILE* 3.2 21.8 + - + +
675S ASP* 3.1 14.6 - - - +
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Residues in contact with MET 672 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670S SER* 3.7 24.0 - - - +
671S ILE* 1.4 86.3 - - + +
673S SER* 1.4 55.7 + - - +
675S ASP* 3.4 12.1 + - - +
676S LYS* 2.8 40.6 + - + +
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Residues in contact with SER 673 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633S ASN* 2.8 41.7 + - - +
636S CYS* 5.4 4.0 - - - -
637S MET* 4.3 6.1 - - - +
660S LEU* 5.0 0.4 - - - -
669S ILE* 4.1 15.7 - - - -
670S SER* 3.2 17.7 + - - -
672S MET* 1.4 75.7 - - - +
674S ILE* 1.4 56.8 + - - +
676S LYS* 3.9 5.5 - - - +
677S ALA* 2.9 35.4 + - - +
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Residues in contact with ILE 674 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 5.6 0.2 - - + -
446A THR* 4.2 12.1 - - + -
447A TYR* 3.4 20.4 - - + +
457A LEU* 4.2 17.5 - - + -
657S MET* 5.5 3.6 - - + +
660S LEU* 3.9 24.0 - - + +
661S VAL* 4.0 17.3 - - + -
664S HIS* 3.8 30.7 - - + +
669S ILE* 3.9 18.2 - - + -
670S SER 4.1 3.1 - - - +
671S ILE* 3.2 12.3 + - - +
673S SER* 1.4 76.9 - - - +
675S ASP* 1.3 55.8 + - - +
677S ALA* 3.8 1.0 - - - +
678S VAL* 3.0 41.0 + - + +
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Residues in contact with ASP 675 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A TYR* 3.2 26.2 + - - -
453A ALA* 4.9 0.2 - - - +
456A ARG* 3.2 45.7 + - - +
457A LEU* 4.1 12.9 - - - +
671S ILE* 3.1 18.4 + - - +
672S MET* 3.4 13.2 + - - +
674S ILE* 1.3 73.4 - - - +
676S LYS* 1.3 52.3 + - - +
678S VAL* 3.0 4.0 + - - +
679S THR* 2.7 40.7 + - - -
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Residues in contact with LYS 676 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637S MET* 3.8 23.5 - - + +
672S MET* 2.8 24.7 + - + +
673S SER* 3.9 4.5 - - - +
675S ASP* 1.3 71.5 - - - +
677S ALA* 1.3 56.2 + - - +
679S THR* 3.7 8.3 - - - -
680S LYS* 3.0 30.5 + - - +
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Residues in contact with ALA 677 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636S CYS* 4.8 4.3 - - + +
637S MET* 3.8 12.2 - - - -
640S VAL* 3.7 28.5 - - + +
656S PHE* 4.3 2.1 - - + -
660S LEU* 4.0 24.5 - - + -
673S SER 2.9 22.1 + - - +
674S ILE 3.8 3.4 - - - +
676S LYS* 1.3 69.2 - - - +
678S VAL* 1.3 60.7 + - - +
680S LYS* 3.6 1.1 + - - +
681S LEU* 3.1 27.9 + - - +
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Residues in contact with VAL 678 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 5.6 1.8 - - - +
457A LEU* 3.8 24.2 - - + -
656S PHE* 5.2 4.3 - - + -
657S MET* 4.4 17.0 - - + -
660S LEU* 3.9 19.1 - - + -
674S ILE* 3.0 25.7 + - + +
675S ASP 3.7 2.7 - - - +
677S ALA* 1.3 71.9 - - - +
679S THR* 1.4 64.2 + - - +
681S LEU* 3.3 8.4 + - + +
682S ARG* 3.1 64.9 + - + +
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Residues in contact with THR 679 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 4.1 18.9 + - - -
675S ASP 2.7 26.2 + - - -
676S LYS* 3.7 9.1 - - - -
678S VAL* 1.4 72.7 - - - +
680S LYS* 1.3 60.9 + - - +
682S ARG* 3.3 10.6 + - - +
683S GLU* 3.2 38.3 + - - +
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Residues in contact with LYS 680 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637S MET* 3.7 26.3 + - + +
640S VAL* 3.9 20.4 - - + -
641S GLU* 2.9 40.3 + - + +
676S LYS 3.0 19.0 + - - +
677S ALA 3.8 5.4 - - - +
678S VAL 3.3 0.2 - - - -
679S THR* 1.3 76.0 - - - +
681S LEU* 1.3 59.1 + - - +
683S GLU* 3.4 19.6 - - + +
684S MET* 3.3 32.6 + - + +
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Residues in contact with LEU 681 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640S VAL* 3.7 11.6 - - + +
644S GLY* 3.6 38.8 - - - +
647S ILE* 3.9 10.3 - - + -
648S ILE* 3.4 17.9 - - + +
653S CYS* 3.8 28.5 - - + +
656S PHE* 3.7 29.2 - - + -
677S ALA 3.1 18.4 + - - +
678S VAL* 3.3 8.3 + - + +
680S LYS* 1.3 74.8 - - - +
682S ARG* 1.4 60.3 + - + +
684S MET* 3.3 6.0 - - - +
685S GLN* 3.1 23.8 + - - +
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Residues in contact with ARG 682 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 3.6 13.4 + - - +
457A LEU 2.7 34.8 + - - -
458A ILE 4.6 1.2 + - - -
459A GLY* 4.5 10.1 - - - +
657S MET* 4.7 2.4 - - - -
678S VAL* 3.1 46.4 + - + +
679S THR* 3.3 8.2 + - - +
681S LEU* 1.4 77.0 - - + +
683S GLU* 1.4 57.6 + - - +
685S GLN* 3.2 17.2 + - - +
686S GLN* 3.1 35.5 + - - +
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Residues in contact with GLU 683 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679S THR* 3.2 31.2 + - - +
680S LYS* 3.4 24.6 - - + +
682S ARG* 1.4 74.8 - - - +
684S MET* 1.3 62.0 + - - +
685S GLN 3.3 0.2 - - - -
686S GLN* 3.4 23.5 - - - +
687S LYS* 3.4 18.9 + - - +
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Residues in contact with MET 684 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640S VAL* 3.5 39.5 - - + +
641S GLU* 4.1 14.6 - - - +
644S GLY* 3.9 18.8 - - - -
645S GLN* 4.3 16.2 - - - +
648S ILE* 4.1 7.6 - - + -
680S LYS* 3.3 29.3 + - + +
681S LEU* 3.3 11.9 - - - +
682S ARG 3.2 0.2 - - - -
683S GLU* 1.3 76.0 - - - +
685S GLN* 1.4 60.7 + - - +
687S LYS* 3.4 23.4 + - + +
688S LEU* 3.5 13.0 - - + +
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Residues in contact with GLN 685 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648S ILE* 3.7 33.4 + - + +
653S CYS* 4.0 19.2 - - - -
681S LEU* 3.1 12.5 + - - +
682S ARG* 3.2 20.4 + - - +
684S MET* 1.4 74.8 - - - +
686S GLN* 1.4 56.0 + - - +
687S LYS 3.3 0.4 - - - -
688S LEU* 3.2 29.2 + - + +
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Residues in contact with GLN 686 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682S ARG* 3.1 25.6 + - - +
683S GLU* 3.4 24.8 - - - +
684S MET 3.3 0.2 - - - -
685S GLN* 1.4 72.8 - - - +
687S LYS* 1.4 56.2 + - - +
688S LEU 3.0 16.4 + - - +
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Residues in contact with LYS 687 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645S GLN* 5.8 3.8 - - - +
683S GLU 3.4 9.3 + - - +
684S MET* 3.4 19.7 - - + +
686S GLN* 1.4 74.7 - - - +
688S LEU* 1.3 65.5 + - + +
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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