Contacts of the helix formed by residues 650 - 670 (chain B) in PDB entry 2HX4
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 ASP 650 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A THR* 2.9 26.1 + - - -
622A SER* 3.6 20.0 + - - -
624A LEU* 4.5 4.3 - - + -
589B MET* 4.1 1.1 - - - -
590B GLY* 4.5 1.8 - - - +
638B LEU* 4.0 30.5 - - + +
649B VAL* 1.3 76.7 - - - +
651B HIS* 1.3 62.2 + - - +
652B HIS* 3.1 8.9 + - - +
653B SER* 2.7 36.8 + - - -
654B ALA* 2.9 26.5 + - - +
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Residues in contact with HIS 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A LEU* 3.6 29.8 - - + -
627A ASP* 2.9 25.4 + - - -
589B MET* 3.7 19.0 - - - +
590B GLY* 5.7 0.2 - - - -
591B THR* 3.2 29.2 + - + +
634B ASN* 5.5 0.4 - - + -
638B LEU* 5.3 1.9 - - + +
650B ASP* 1.3 72.0 - - - +
652B HIS* 1.3 78.7 + + - +
655B THR* 2.6 40.2 + - - +
681B PRO* 3.8 23.3 - - + -
683B MET* 4.1 20.5 - - - +
684B SER* 4.5 0.7 - - - -
688B THR* 4.1 12.1 - - + -
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Residues in contact with HIS 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR* 4.0 33.7 - - + -
624A LEU* 4.2 4.7 - - + -
626A LYS* 4.2 20.3 + - + +
627A ASP* 2.6 38.5 + - - -
650B ASP* 3.1 10.0 + - - +
651B HIS* 1.3 91.9 + + - +
653B SER* 1.3 63.6 + - - +
655B THR* 3.1 6.5 + - - -
656B GLU* 3.0 27.2 + - - +
687B ILE* 4.0 33.5 + - + -
688B THR* 4.3 4.4 - - + +
689B PRO* 4.7 4.0 - - + +
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Residues in contact with SER 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR* 4.3 8.2 + - - -
649B VAL* 3.5 12.9 - - - +
650B ASP* 2.7 33.7 + - - -
652B HIS* 1.3 74.2 - - - +
654B ALA* 1.3 62.0 + - - +
656B GLU* 3.4 8.9 + - - +
657B SER* 3.1 29.3 + - - -
860B ACT 5.1 0.5 + - - -
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Residues in contact with ALA 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B VAL* 4.1 13.6 - - + +
589B MET* 3.5 25.1 - - - -
649B VAL* 3.6 20.8 - - + +
650B ASP 2.9 22.3 + - - +
651B HIS 4.2 0.2 - - - +
653B SER* 1.3 73.4 + - - +
655B THR* 1.3 62.8 + - - +
657B SER* 3.3 4.2 + - - -
658B PHE* 3.1 21.3 + - - +
750B HEM 5.7 0.7 - - + -
860B ACT 4.0 13.3 - - + +
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Residues in contact with THR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B VAL* 4.3 17.0 - - + -
589B MET* 5.0 2.7 - - - -
651B HIS* 2.6 29.8 + - - +
652B HIS 3.1 8.0 + - - -
654B ALA* 1.3 72.8 - - - +
656B GLU* 1.3 64.5 + - - +
658B PHE* 3.2 3.7 + - - +
659B ILE* 3.1 26.5 + - - +
679B ILE 4.6 0.7 - - - +
681B PRO* 3.5 28.9 - - + -
688B THR* 3.5 6.1 - - - -
689B PRO* 3.3 17.4 - - - +
690B VAL* 3.7 27.1 - - + +
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Residues in contact with GLU 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A THR* 6.0 1.6 - - - +
652B HIS 3.0 19.8 + - - +
653B SER* 3.7 9.0 - - - +
654B ALA 3.3 0.2 - - - -
655B THR* 1.3 76.8 + - - +
657B SER* 1.3 63.7 + - - +
659B ILE* 3.3 5.6 + - + +
660B LYS* 3.2 53.1 + - + +
689B PRO* 3.8 15.7 - - + -
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Residues in contact with SER 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ILE* 3.8 26.4 - - - +
653B SER* 3.1 17.2 + - - -
654B ALA 3.5 9.0 - - - -
655B THR 3.2 0.2 - - - -
656B GLU* 1.3 78.1 - - - +
658B PHE* 1.3 51.8 + - - +
660B LYS* 3.2 11.0 + - - +
661B HIS* 2.7 35.3 + - - +
860B ACT 3.9 18.0 + - - -
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Residues in contact with PHE 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B CYS 3.7 7.6 - - - -
416B VAL* 3.5 44.1 + - + +
418B ARG* 3.5 35.0 - - - -
419B ILE* 5.5 1.1 - - - -
654B ALA 3.1 6.6 + - - +
655B THR 3.2 7.8 + - - +
657B SER* 1.3 77.2 - - - +
659B ILE* 1.3 53.3 + - + +
661B HIS* 3.5 22.2 - + - +
662B MET* 2.7 55.7 + - + +
672B CYS* 4.4 8.1 - - - -
674B ALA* 4.0 11.7 - - + -
679B ILE* 4.0 17.3 - - + -
690B VAL* 3.8 19.3 - - + -
695B MET* 4.2 7.9 - - + -
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Residues in contact with ILE 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ASN* 4.7 6.1 - - - +
655B THR 3.1 17.1 + - - +
656B GLU* 3.6 8.7 - - + +
657B SER 3.2 0.2 - - - -
658B PHE* 1.3 80.1 - - + +
660B LYS* 1.3 61.8 + - + +
662B MET* 3.2 6.2 + - - +
663B GLU* 2.9 48.6 + - + +
689B PRO* 4.0 23.6 - - + +
690B VAL* 3.8 20.2 - - + -
693B GLN* 3.7 42.2 - - + +
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Residues in contact with LYS 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ILE* 5.1 5.4 - - + -
656B GLU* 3.2 46.2 + - + +
657B SER* 3.5 9.4 - - - +
659B ILE* 1.3 77.9 - - + +
661B HIS* 1.3 63.3 + - - +
663B GLU* 3.4 13.2 + - - +
664B ASN* 3.0 25.0 + - - +
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Residues in contact with HIS 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ARG* 5.3 2.2 + - + -
418B ARG* 3.5 38.9 - - + +
419B ILE* 3.5 33.5 + - + +
421B TRP* 3.8 13.9 - + - -
657B SER 2.7 20.5 + - - +
658B PHE* 3.5 22.7 - + - +
660B LYS* 1.3 74.0 - - - +
662B MET* 1.3 57.7 + - - +
664B ASN* 3.3 11.2 + - - +
665B GLU* 2.9 61.8 + - + +
672B CYS* 4.1 10.4 - - - -
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Residues in contact with MET 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B VAL* 4.4 1.8 - - + -
312B LEU* 5.0 3.4 - - + -
658B PHE* 2.7 43.5 + - + +
659B ILE* 3.5 8.5 - - - +
661B HIS* 1.3 76.0 - - - +
663B GLU* 1.3 67.3 + - + +
665B GLU* 3.0 5.9 + - - +
666B TYR* 3.0 62.9 + - + +
672B CYS* 4.1 17.3 - - + +
674B ALA* 5.1 1.1 - - + -
693B GLN* 3.9 27.4 - - - +
694B GLU 3.6 23.3 - - - +
695B MET* 4.2 13.7 - - + -
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Residues in contact with GLU 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ASN* 6.2 0.2 - - - +
308B THR* 5.4 0.9 + - - -
310B VAL* 3.9 21.3 - - - +
312B LEU* 4.0 24.9 - - + -
659B ILE* 2.9 34.7 + - + +
660B LYS* 3.8 12.4 - - - +
662B MET* 1.3 76.5 - - + +
664B ASN* 1.3 64.8 + - - +
666B TYR* 3.2 2.8 + - - +
667B ARG* 3.2 59.0 + - - +
693B GLN* 5.3 3.4 - - - +
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Residues in contact with ASN 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B LYS 3.0 13.9 + - - +
661B HIS* 3.4 15.8 + - - +
663B GLU* 1.3 78.2 - - - +
665B GLU* 1.3 66.1 + - - +
667B ARG* 3.3 7.9 + - - +
668B CYS* 2.8 41.1 + - - +
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Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ARG* 2.8 52.0 + - - +
421B TRP* 4.3 3.6 + - - -
661B HIS* 2.9 47.0 + - + +
662B MET 3.0 7.4 + - - +
664B ASN* 1.3 79.4 + - + +
666B TYR* 1.3 58.8 + - - +
668B CYS* 3.7 8.1 - - - -
669B ARG* 2.7 41.8 + - - +
670B GLY 3.0 4.9 + - - -
671B GLY 3.4 13.9 + - - +
672B CYS* 3.7 12.5 - - + -
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Residues in contact with TYR 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B VAL* 3.8 27.9 - - + +
312B LEU* 3.5 39.0 - - + -
313B THR 3.1 25.2 - - - +
314B ASP* 3.6 36.8 + - + +
662B MET* 3.0 54.1 + - + +
663B GLU 3.2 6.9 + - - +
665B GLU* 1.3 74.6 - - - +
667B ARG* 1.3 59.7 + - + +
670B GLY* 2.7 27.0 + - - -
671B GLY* 3.4 10.1 - - - +
672B CYS* 3.7 21.8 + - + -
696B LEU* 4.3 7.6 + - - +
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Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 4.3 11.1 - - - +
312B LEU* 3.9 22.0 - - + +
663B GLU* 3.2 52.3 + - - +
664B ASN* 3.8 7.5 - - - +
666B TYR* 1.3 81.8 - - + +
668B CYS* 1.3 59.5 + - - +
669B ARG 3.8 0.2 + - - -
670B GLY 4.7 0.7 + - - -
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Residues in contact with CYS 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ARG* 3.8 12.6 - - - -
664B ASN* 2.8 36.6 + - - +
665B GLU* 3.7 22.0 - - - -
667B ARG* 1.3 74.7 - - - +
669B ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B THR* 4.9 0.3 + - - -
316B LEU* 3.6 44.7 - - + +
407B HIS* 3.9 17.6 - - - -
410B ARG* 3.6 57.2 + - - +
411B ASN* 2.9 33.7 + - - +
665B GLU* 2.7 29.0 + - - +
668B CYS* 1.3 76.2 - - - +
670B GLY* 1.3 60.2 + - - +
671B GLY 4.0 2.4 + - - +
672B CYS* 5.7 0.2 - - - +
673B PRO* 4.8 4.8 - - - +
700B LEU* 4.0 8.7 - - - +
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Residues in contact with GLY 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR 4.3 5.4 - - - -
314B ASP* 3.4 2.9 - - - -
315B THR* 2.8 42.0 + - - -
316B LEU* 2.8 9.0 + - - -
666B TYR* 2.7 25.1 + - - -
667B ARG 4.5 0.6 + - - -
668B CYS 3.9 0.4 - - - -
669B ARG* 1.3 73.8 - - - +
671B GLY* 1.3 56.6 + - - +
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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
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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