Contacts of the helix formed by residues 670 - 687 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ARG* 4.9 4.9 - - - +
633T ASN* 3.0 13.9 + - - +
664T HIS* 4.1 2.2 - - - -
669T ILE* 1.4 79.4 - - - +
671T ILE* 1.3 67.3 + - - +
672T MET* 3.7 27.7 - - - +
673T SER* 3.2 35.3 + - - -
674T ILE* 3.6 5.9 + - - +
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Residues in contact with ILE 671 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ARG* 5.6 4.5 - - - +
446B THR* 4.5 13.9 - - + +
447B TYR* 3.5 36.5 + - + +
664T HIS* 3.5 24.2 + - + -
670T SER* 1.3 77.3 - - - +
672T MET* 1.4 73.7 + - + +
674T ILE* 3.2 20.4 + - + +
675T ASP* 3.1 15.2 - - - +
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Residues in contact with MET 672 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670T SER* 3.7 24.2 - - - +
671T ILE* 1.4 86.7 - - + +
673T SER* 1.4 60.2 + - - +
675T ASP* 3.3 12.0 + - - +
676T LYS* 2.8 36.5 + - + +
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Residues in contact with SER 673 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633T ASN* 2.8 40.5 + - - +
636T CYS* 5.4 3.5 - - - +
637T MET* 4.3 7.5 - - - +
660T LEU* 5.0 0.4 - - - -
669T ILE* 4.1 15.3 - - - -
670T SER* 3.2 18.4 + - - -
672T MET* 1.4 77.3 - - - +
674T ILE* 1.4 55.3 + - - +
676T LYS* 3.9 5.1 - - - +
677T ALA* 2.9 35.3 + - - +
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Residues in contact with ILE 674 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 5.8 0.7 - - + -
446B THR* 4.1 18.4 - - + -
447B TYR* 3.6 17.5 - - + +
457B LEU* 4.1 17.7 - - + -
657T MET* 5.5 2.2 - - + +
660T LEU* 3.9 23.3 - - + +
661T VAL* 4.0 18.6 - - + -
664T HIS* 3.8 28.3 - - + +
669T ILE* 3.9 17.9 - - + -
670T SER 4.1 3.4 - - - +
671T ILE* 3.2 12.8 + - - +
673T SER* 1.4 76.0 - - - +
675T ASP* 1.3 56.2 + - - +
677T ALA* 3.8 1.0 - - - +
678T VAL* 3.0 40.3 + - + +
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Residues in contact with ASP 675 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B TYR* 2.7 31.6 + - - -
453B ALA* 4.8 0.2 - - - +
456B ARG* 3.4 42.9 + - - +
457B LEU* 4.1 10.2 - - - +
671T ILE* 3.1 15.4 + - - +
672T MET* 3.3 13.2 + - - +
674T ILE* 1.3 74.1 - - - +
676T LYS* 1.4 53.0 + - - +
678T VAL* 3.0 7.5 + - - +
679T THR* 2.8 40.0 + - - -
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Residues in contact with LYS 676 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637T MET* 3.8 23.6 - - + -
672T MET* 2.8 25.4 + - + +
673T SER* 3.9 4.9 - - - +
675T ASP* 1.4 70.4 - - - +
677T ALA* 1.4 56.7 + - - +
679T THR* 3.6 6.6 + - - -
680T LYS* 3.0 30.5 + - - +
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Residues in contact with ALA 677 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636T CYS* 4.8 2.9 - - + +
637T MET* 3.8 12.7 - - - -
640T VAL* 3.7 28.9 - - + +
656T PHE* 4.4 1.7 - - - -
660T LEU* 4.0 25.4 - - + -
673T SER 2.9 21.8 + - - +
674T ILE 3.8 3.1 - - - +
676T LYS* 1.4 69.8 - - - +
678T VAL* 1.4 60.7 + - - +
680T LYS* 3.5 1.1 + - - +
681T LEU* 3.1 28.1 + - - +
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Residues in contact with VAL 678 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG 5.3 0.9 - - - +
457B LEU* 3.7 27.1 - - + -
656T PHE* 5.2 4.3 - - + -
657T MET* 4.3 13.2 - - + -
660T LEU* 3.9 19.3 - - + -
674T ILE* 3.0 23.9 + - + +
675T ASP* 3.7 2.9 - - - +
677T ALA* 1.4 72.3 - - - +
679T THR* 1.3 66.0 + - - +
681T LEU* 3.3 8.4 + - + +
682T ARG* 3.1 64.5 + - + +
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Residues in contact with THR 679 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG* 4.7 12.3 + - - +
675T ASP* 2.8 32.6 + - - +
676T LYS* 3.7 7.6 - - + -
678T VAL* 1.3 72.1 - - - +
680T LYS* 1.4 60.3 + - - +
682T ARG* 3.3 10.4 + - - +
683T GLU* 3.2 39.1 + - - +
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Residues in contact with LYS 680 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637T MET* 3.7 26.4 - - + +
640T VAL* 3.9 20.9 - - + -
641T GLU* 2.9 41.2 + - + +
676T LYS 3.0 17.4 + - - +
677T ALA 3.8 5.4 - - - +
678T VAL 3.3 0.2 - - - -
679T THR* 1.4 76.0 - - - +
681T LEU* 1.3 59.2 + - - +
683T GLU* 3.4 18.7 - - + +
684T MET* 3.3 33.6 + - + +
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Residues in contact with LEU 681 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640T VAL* 3.7 12.3 - - + +
644T GLY* 3.6 39.3 - - - +
647T ILE* 3.9 17.9 - - + -
648T ILE* 3.4 17.9 - - + +
653T CYS* 3.9 21.3 - - + +
656T PHE* 3.7 28.7 - - + -
677T ALA 3.1 17.7 + - - +
678T VAL* 3.3 8.9 + - + +
680T LYS* 1.3 73.9 - - - +
682T ARG* 1.4 59.9 + - + +
684T MET* 3.3 6.6 - - - +
685T GLN* 3.1 23.9 + - - +
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Residues in contact with ARG 682 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG 3.7 11.7 + - - -
457B LEU 2.7 34.1 + - - -
458B ILE 4.8 1.4 + - - -
459B GLY* 4.6 9.0 - - - +
657T MET* 4.6 3.4 - - - -
678T VAL* 3.1 43.1 + - + +
679T THR* 3.3 9.2 + - - +
681T LEU* 1.4 75.7 - - + +
683T GLU* 1.4 59.1 + - - +
685T GLN* 3.2 17.8 + - - +
686T GLN* 3.1 36.2 + - - +
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Residues in contact with GLU 683 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679T THR* 3.2 31.3 + - - +
680T LYS* 3.4 25.1 - - + +
682T ARG* 1.4 74.4 - - - +
684T MET* 1.3 61.4 + - - +
685T GLN 3.3 0.2 - - - -
686T GLN* 3.4 24.2 - - - +
687T LYS* 3.3 18.9 + - - +
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Residues in contact with MET 684 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640T VAL* 3.6 40.6 - - + +
641T GLU* 4.1 14.4 - - + +
644T GLY* 3.9 18.6 - - - -
645T GLN* 4.3 15.2 - - - +
648T ILE* 4.1 7.9 - - + -
680T LYS* 3.3 34.5 + - + +
681T LEU* 3.3 11.4 - - - +
683T GLU* 1.3 75.1 - - - +
685T GLN* 1.4 60.2 + - - +
686T GLN 3.3 0.2 - - - -
687T LYS* 3.4 23.0 - - + +
688T LEU* 3.5 13.6 - - + +
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Residues in contact with GLN 685 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648T ILE* 3.7 34.2 - - + +
653T CYS* 4.0 19.0 - - - -
681T LEU* 3.1 12.7 + - - +
682T ARG* 3.2 21.5 + - - +
684T MET* 1.4 75.6 - - - +
686T GLN* 1.4 57.1 + - - +
687T LYS 3.3 0.4 - - - -
688T LEU* 3.2 28.8 + - + +
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Residues in contact with GLN 686 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682T ARG* 3.1 26.4 + - - +
683T GLU* 3.4 25.5 - - - +
685T GLN* 1.4 72.8 - - - +
687T LYS* 1.4 55.6 + - - +
688T LEU 3.0 16.3 + - - +
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Residues in contact with LYS 687 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645T GLN* 5.7 5.7 + - - +
683T GLU 3.3 9.2 + - - +
684T MET* 3.4 19.7 - - + +
685T GLN 3.3 0.2 - - - -
686T GLN* 1.4 75.6 - - - +
688T LEU* 1.4 65.6 + - + +
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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