Contacts of the helix formed by residues 656 - 675 (chain B) in PDB entry 1HWL
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 GLY 656 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B MET* 3.9 5.2 - - - -
651B SER* 3.7 19.3 - - - -
654B ALA* 3.0 9.1 - - - +
655B MET* 1.3 80.9 - - - +
657B MET* 1.3 59.4 + - - +
658B ASN 3.3 2.7 - - - -
659B MET* 3.3 7.7 + - - +
660B ILE* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B FBI 4.3 1.8 - - - -
588B MET* 4.1 8.1 - - + -
589B THR 3.1 28.5 - - - +
590B ARG* 3.5 39.9 - - + +
655B MET* 3.4 35.0 - - + +
656B GLY* 1.3 74.6 - - - +
658B ASN* 1.3 62.7 + - - +
660B ILE* 3.4 3.5 + - + +
661B SER* 2.9 34.8 + - - -
690B ASP* 3.7 18.4 - - - +
702B ARG* 3.2 17.5 - - - +
770B GLN* 4.1 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B GLY 3.3 0.4 - - - -
657B MET* 1.3 79.0 - - - +
659B MET* 1.3 65.4 + - - +
661B SER* 3.2 7.5 + - - -
662B LYS* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B PHE* 5.2 0.7 - - - -
625B THR* 4.7 2.1 + - - -
626B SER* 4.1 24.2 - - - +
628B PHE* 3.7 39.3 - - + -
629B ALA* 4.3 7.4 - - + +
650B ARG 4.4 2.0 - - - +
651B SER* 3.6 40.2 - - - +
654B ALA* 4.4 13.5 - - + -
656B GLY* 3.3 9.0 + - - +
658B ASN* 1.3 79.7 - - - +
660B ILE* 1.3 65.5 + - + +
662B LYS* 3.2 11.9 + - - +
663B GLY* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B MET* 3.9 21.3 - - + +
589B THR* 4.1 4.3 - - - -
590B ARG* 3.7 33.0 - - + +
622B PHE* 3.8 15.3 - - + -
629B ALA* 5.9 0.2 - - - -
647B PHE 4.4 5.6 - - - +
649B SER* 3.5 43.3 - - - +
650B ARG 4.2 5.2 - - - +
651B SER* 4.9 4.5 - - - -
656B GLY* 2.8 26.1 + - - +
657B MET* 3.9 4.5 - - + +
659B MET* 1.3 76.2 - - + +
661B SER* 1.3 57.3 + - - +
663B GLY* 3.4 1.0 + - - -
664B THR* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B FBI 4.0 16.1 - - - -
590B ARG* 3.2 33.0 + - - -
657B MET 2.9 22.5 + - - -
658B ASN* 3.5 7.9 - - - -
660B ILE* 1.3 74.0 - - - +
662B LYS* 1.3 65.5 + - - +
664B THR* 3.1 7.5 + - - -
665B GLU* 2.9 34.0 + - - +
683B VAL* 4.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B THR* 3.4 35.6 + - - +
626B SER* 5.4 3.3 - - - -
658B ASN* 3.0 17.4 + - + +
659B MET* 3.5 12.1 - - - +
661B SER* 1.3 76.7 - - - +
663B GLY* 1.3 64.2 + - - +
665B GLU* 3.3 13.0 + - - +
666B LYS* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B PHE* 3.3 38.3 - - - -
625B THR* 3.4 19.6 + - - -
659B MET 3.0 10.1 + - - -
660B ILE 3.8 0.2 - - - -
662B LYS* 1.3 81.2 - - - +
664B THR* 1.3 55.2 + - - +
666B LYS* 3.4 1.0 + - - -
667B ALA* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B ARG* 3.7 19.1 - - + +
592B PRO* 3.7 34.5 - - + -
622B PHE* 3.5 5.4 - - - -
647B PHE* 3.8 25.1 - - + +
660B ILE 2.8 23.4 + - - -
661B SER* 3.1 8.0 + - - -
663B GLY* 1.3 74.8 - - - +
665B GLU* 1.3 59.2 + - - +
667B ALA* 3.3 3.6 + - - +
668B LEU* 2.8 42.6 + - + +
683B VAL* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B FBI 6.5 0.7 - - - -
661B SER* 2.9 23.4 + - - +
662B LYS* 3.3 14.3 + - - +
664B THR* 1.3 76.2 - - - +
666B LYS* 1.3 62.7 + - - +
668B LEU* 3.3 10.0 + - - +
669B SER* 3.0 23.7 + - - -
680B ILE* 5.5 0.7 - - - +
683B VAL* 4.0 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ALA* 3.5 17.0 - - + +
624B SER* 2.7 32.1 + - - -
625B THR* 3.3 35.7 - - + -
662B LYS 3.2 5.1 + - - +
663B GLY 4.0 0.9 - - - +
665B GLU* 1.3 79.1 - - - +
667B ALA* 1.3 63.8 + - - +
669B SER* 3.1 10.5 + - - -
670B LYS* 3.1 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ILE* 3.7 18.7 - - + +
621B ALA* 4.2 11.8 - - - +
622B PHE* 4.2 11.2 - - + -
647B PHE* 3.6 29.6 - - + -
663B GLY 2.9 18.8 + - - +
664B THR 3.3 1.8 + - - +
666B LYS* 1.3 76.9 - - - +
668B LEU* 1.3 58.9 + - - +
670B LYS* 3.3 3.8 + - - +
671B LEU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B PRO* 3.9 25.4 - - + -
594B VAL* 4.2 18.8 - - + -
645B ILE* 4.4 9.9 - - + -
647B PHE* 4.1 22.7 - - + -
664B THR* 2.8 32.8 + - + +
665B GLU* 3.7 8.1 - - - +
666B LYS 3.2 0.2 - - - -
667B ALA* 1.3 74.2 - - - +
669B SER* 1.3 58.7 + - - +
671B LEU* 3.3 12.0 + - + +
672B HIS* 2.9 28.2 + - - +
678B MET* 3.6 4.7 - - + +
680B ILE* 3.7 38.3 - - + +
683B VAL* 5.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B GLU 3.0 15.4 + - - -
666B LYS* 3.1 15.7 + - - -
668B LEU* 1.3 76.2 - - - +
670B LYS* 1.3 63.3 + - - +
672B HIS* 3.0 18.4 + - - +
673B GLU* 3.2 19.5 + - - +
680B ILE* 4.9 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B VAL* 3.7 25.6 - - + +
618B ILE* 4.4 5.2 - - + -
621B ALA* 3.7 29.6 - - + -
666B LYS* 3.1 4.1 + - - +
667B ALA 3.6 7.4 - - - +
669B SER* 1.3 80.4 - - - +
671B LEU* 1.3 61.4 + - - +
673B GLU* 3.1 45.0 + - - +
674B TYR* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B VAL* 4.1 11.9 - - + -
608B TRP* 3.7 31.0 - - + -
609B LEU* 4.1 11.9 - - + -
618B ILE* 4.0 6.9 - - + +
645B ILE* 4.1 24.9 - - + -
647B PHE* 6.2 0.9 - - + -
667B ALA 3.0 15.5 + - - +
668B LEU* 3.6 15.3 - - + +
669B SER 3.2 0.2 - - - -
670B LYS* 1.3 75.6 - - - +
672B HIS* 1.3 62.6 + - - +
674B TYR* 3.0 9.1 + - + +
675B PHE* 3.0 36.5 + - + +
678B MET* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LEU 2.9 13.8 + - - +
669B SER* 3.0 14.8 + - - +
671B LEU* 1.3 77.6 - - - +
673B GLU* 1.3 61.0 + - - +
675B PHE 3.1 7.8 - - - -
676B PRO* 3.0 54.7 + - + +
678B MET* 3.1 34.6 + - + +
680B ILE* 5.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B SER* 3.2 15.6 + - - +
670B LYS* 3.1 47.5 + - - +
672B HIS* 1.3 78.5 - - - +
674B TYR* 1.3 65.8 + - + +
676B PRO* 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B TRP* 3.6 35.0 - + + -
617B VAL* 3.6 40.7 - - + +
670B LYS* 3.4 25.4 - - + -
671B LEU 3.0 7.4 + - - +
673B GLU* 1.3 84.5 - - + +
675B PHE* 1.3 82.9 + - + +
676B PRO* 3.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 4.8 5.2 - - + -
604B GLU* 4.1 30.7 - - + -
605B VAL* 3.6 31.4 - - + -
608B TRP* 3.9 44.0 - + + -
671B LEU* 3.0 26.4 + - + +
672B HIS* 3.1 10.2 - - - +
674B TYR* 1.3 100.5 - - + +
676B PRO* 1.3 62.1 - - - +
677B GLU* 3.2 3.1 - - + -
678B MET* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
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