Contacts of the helix formed by residues 631 - 650 (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 GLN 631 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B TRP* 3.4 42.0 - - + +
625T GLY 4.8 0.5 + - - +
626T PHE* 3.6 29.5 - - + +
627T ILE* 2.8 41.2 - - - +
628T ALA* 3.0 21.1 - - + +
629T ASP 3.1 0.8 - - - -
630T ASN* 1.4 90.0 - - - +
632T MET* 1.4 59.1 + - - +
633T ASN 3.4 1.6 - - - -
634T HIS* 3.5 12.1 + - + +
635T ALA* 2.9 29.5 + - - +
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Residues in contact with MET 632 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.6 51.4 - - + -
617T TRP* 3.3 32.1 - - + -
626T PHE* 5.0 6.5 - - - -
628T ALA 4.2 2.9 - - - +
629T ASP 2.9 17.1 + - - +
631T GLN* 1.4 77.5 - - - +
633T ASN* 1.4 65.1 + - - +
635T ALA* 3.3 12.8 + - - +
636T CYS* 3.2 26.9 + - - -
663T MET* 3.7 21.8 - - + -
668T LEU* 3.4 30.7 - - + +
669T ILE* 3.7 3.4 - - + -
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Residues in contact with ASN 633 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629T ASP 5.0 2.0 + - - -
630T ASN* 4.4 12.7 + - - +
631T GLN 3.4 0.6 - - - -
632T MET* 1.4 74.8 - - - +
634T HIS* 1.4 62.8 + - - +
636T CYS* 3.3 13.7 + - - +
637T MET* 3.3 18.5 + - - +
668T LEU 4.1 8.3 + - - -
669T ILE* 3.4 10.1 - - - +
670T SER* 3.0 27.8 + - - +
673T SER* 2.8 27.6 + - - +
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Residues in contact with HIS 634 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626T PHE* 4.3 12.8 - + - -
630T ASN 5.0 2.0 + - - +
631T GLN* 3.5 13.1 + - + +
632T MET 3.4 0.2 - - - -
633T ASN* 1.4 78.0 - - - +
635T ALA* 1.4 54.4 + - - +
637T MET* 3.3 10.8 + - - +
638T LEU* 2.9 66.9 + - + +
641T GLU* 5.8 2.9 - - - -
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Residues in contact with ALA 635 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617T TRP* 3.9 14.8 - - + -
620T HIS* 2.8 23.7 + - - -
626T PHE* 3.6 39.7 - - + -
631T GLN 2.9 19.4 + - - +
632T MET* 3.4 13.5 - - - +
634T HIS* 1.4 74.5 - - - +
636T CYS* 1.4 57.4 + - - +
638T LEU* 4.5 0.9 - - - -
639T PHE* 2.9 13.5 + - - +
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Residues in contact with CYS 636 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617T TRP* 3.9 5.8 - - - -
632T MET 3.2 14.6 + - - -
633T ASN* 3.3 8.2 + - - +
635T ALA* 1.4 76.0 - - - +
637T MET* 1.3 68.2 + - - +
639T PHE* 3.2 9.7 + - - +
640T VAL* 3.1 27.8 + - - +
656T PHE* 4.8 1.9 - - + -
659T HIS* 4.8 1.1 - - - -
660T LEU* 4.1 27.4 - - + -
663T MET* 3.5 32.3 - - - -
669T ILE* 3.6 16.2 - - + -
673T SER* 5.4 3.8 - - - -
677T ALA* 5.1 2.9 - - + -
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Residues in contact with MET 637 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633T ASN* 3.3 13.9 + - + +
634T HIS* 3.3 14.0 + - + +
636T CYS* 1.3 76.6 - - - +
638T LEU* 1.4 56.4 + - - +
640T VAL* 3.1 20.6 + - + +
641T GLU* 3.2 24.4 + - - +
673T SER* 4.3 8.5 - - - +
676T LYS* 3.8 37.7 - - + +
677T ALA* 3.8 25.1 - - - +
680T LYS* 3.7 35.9 + - + +
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Residues in contact with LEU 638 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620T HIS* 3.7 7.8 - - + -
624T HIS* 3.6 34.1 - - + +
626T PHE* 4.0 9.0 - - + -
634T HIS* 2.9 43.8 + - + +
635T ALA 3.9 4.0 - - - +
637T MET* 1.4 70.6 - - - +
639T PHE* 1.4 59.4 + - - +
641T GLU* 3.5 24.6 + - - +
642T ASN* 3.0 59.3 + - - +
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Residues in contact with PHE 639 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613T VAL* 4.5 6.5 - - + -
616T LEU* 3.4 44.4 - - + -
617T TRP* 3.7 29.6 - + + -
620T HIS* 3.6 17.5 - + - +
635T ALA 2.9 18.6 + - - +
636T CYS 3.3 6.5 - - - +
637T MET 3.2 0.4 - - - -
638T LEU* 1.4 75.5 - - - +
640T VAL* 1.4 54.3 - - - +
643T TYR* 2.7 60.6 + + + +
644T GLY 3.6 0.5 + - - -
647T ILE* 4.2 17.3 - - + -
656T PHE* 3.5 38.4 - + - -
659T HIS* 5.2 1.6 - - - -
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Residues in contact with VAL 640 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636T CYS 3.1 14.8 + - - +
637T MET* 3.1 8.4 + - - +
639T PHE* 1.4 73.5 - - - +
641T GLU* 1.4 61.8 + - - +
644T GLY* 2.8 33.6 + - - +
656T PHE* 3.6 26.0 - - + -
677T ALA* 3.7 22.4 - - + +
680T LYS* 3.9 10.1 - - + -
681T LEU* 3.7 40.8 - - + +
684T MET* 3.6 15.0 - - + +
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Residues in contact with GLU 641 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634T HIS* 5.8 2.8 - - - -
637T MET* 3.4 20.2 - - - +
638T LEU* 3.5 27.3 + - - +
639T PHE 3.5 0.2 - - - -
640T VAL* 1.4 78.7 - - - +
642T ASN* 1.3 68.0 + - - +
644T GLY 4.5 0.9 + - - -
645T GLN 5.5 0.5 + - - -
680T LYS* 2.9 33.9 + - - +
684T MET* 4.1 16.9 - - + +
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Residues in contact with ASN 642 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620T HIS* 4.3 0.2 - - - -
624T HIS* 3.8 16.8 + - - -
638T LEU* 3.0 41.5 + - - +
641T GLU* 1.3 88.0 + - - +
643T TYR* 1.3 77.2 + - + +
644T GLY 3.7 0.4 - - - -
645T GLN* 5.2 4.0 + - - +
646T LYS* 5.4 3.1 - - - +
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Residues in contact with TYR 643 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616T LEU* 3.7 38.8 - - + -
619T LEU* 3.9 14.8 + - + +
620T HIS* 3.6 37.4 + - + -
623T LYS* 5.2 7.8 - - - +
624T HIS* 5.7 1.1 - + - -
639T PHE* 2.7 51.3 + + + +
642T ASN* 1.3 86.2 - - + +
644T GLY* 1.3 61.9 + - - +
645T GLN 3.3 2.5 - - - -
646T LYS* 3.0 19.1 + - + +
647T ILE* 3.0 23.9 + - + +
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Residues in contact with GLY 644 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639T PHE 3.6 1.6 + - - -
640T VAL* 2.8 28.5 + - - -
641T GLU 4.5 0.6 + - - -
642T ASN 3.7 0.8 - - - -
643T TYR* 1.3 71.1 - - - +
645T GLN* 1.3 56.7 + - - +
647T ILE* 3.3 4.9 + - - +
648T ILE* 3.0 38.3 + - - +
681T LEU* 3.7 20.6 - - - -
684T MET* 3.9 5.8 - - - -
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Residues in contact with GLN 645 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641T GLU 5.5 0.8 + - - -
642T ASN 5.2 3.1 + - - +
643T TYR 3.3 0.8 - - - -
644T GLY* 1.3 74.5 - - - +
646T LYS* 1.4 62.6 + - + +
648T ILE* 4.1 6.7 - - - +
649T LYS* 3.0 67.6 + - + +
684T MET* 4.3 18.9 - - - +
687T LYS* 5.7 5.5 + - - +
688T LEU* 4.4 15.7 - - + +
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Residues in contact with LYS 646 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616T LEU* 4.4 15.9 - - + -
642T ASN 5.4 2.2 - - - +
643T TYR* 3.0 22.5 + - + +
645T GLN* 1.4 78.5 - - + +
647T ILE* 1.3 55.8 + - - +
649T LYS* 4.7 7.6 - - + +
650T LYS* 2.8 62.5 + - + +
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Residues in contact with ILE 647 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613T VAL* 4.3 12.6 - - + -
616T LEU* 3.8 23.6 - - + -
639T PHE* 4.2 23.3 - - + -
643T TYR 3.0 20.9 + - - +
644T GLY* 3.3 9.6 + - - +
646T LYS* 1.3 75.2 - - - +
648T ILE* 1.4 60.9 + - - +
650T LYS 3.8 0.3 - - - -
651T ASN 3.1 4.9 + - - -
652T LEU* 2.9 63.2 + - + +
653T CYS* 3.9 2.6 + - - +
656T PHE* 4.2 11.7 - - + -
681T LEU* 3.9 28.9 - - + -
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Residues in contact with ILE 648 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644T GLY 3.0 23.6 + - - +
645T GLN* 4.1 2.9 - - - +
647T ILE* 1.4 73.6 - - - +
649T LYS* 1.4 60.7 + - + +
651T ASN* 3.0 21.5 + - - +
653T CYS* 4.0 17.8 - - - -
681T LEU* 3.4 37.7 - - + +
684T MET* 4.1 10.5 - - + -
685T GLN* 3.7 46.2 + - + +
688T LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 649 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645T GLN* 3.0 49.0 + - + +
646T LYS* 4.1 8.3 - - + +
648T ILE* 1.4 80.1 - - + +
650T LYS* 1.3 61.6 + - + +
651T ASN* 3.2 2.6 + - - +
688T LEU* 3.5 26.2 - - + +
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Residues in contact with LYS 650 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612T GLU* 3.6 34.5 + - + -
616T LEU* 5.0 4.9 - - + -
646T LYS* 2.8 49.7 + - + +
649T LYS* 1.3 74.4 - - + +
651T ASN* 1.4 69.7 + - - +
652T LEU* 3.7 21.9 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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