Contacts of the helix formed by residues 648 - 661 (chain B) in PDB entry 1JPW
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 ASN 648 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B GLU* 3.5 42.5 + - - +
609B ASN* 5.3 1.8 + - - +
612B ARG* 4.8 7.1 - - - +
646B SER* 2.9 15.7 + - - +
647B ARG* 1.3 76.0 - - - +
649B GLU* 1.3 64.5 + - - +
650B GLY* 2.8 30.3 + - - -
651B VAL* 3.1 19.1 + - + +
652B ALA* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B SER 5.2 0.2 - - - -
647B ARG 3.3 7.2 + - - +
648B ASN* 1.3 71.9 + - - +
650B GLY* 1.3 50.8 + - - +
652B ALA* 3.3 6.7 + - - +
653B THR* 2.5 46.2 + - - +
364C GLN 5.1 1.3 - - - +
367C GLY 4.3 15.7 - - - +
368C LEU* 4.0 19.1 - - + -
400C GLY* 5.4 10.1 - - - -
401C LEU 6.0 0.7 - - - +
404C THR* 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ARG* 4.0 19.5 - - - -
648B ASN* 2.8 15.7 + - - -
649B GLU* 1.3 73.1 - - - +
651B VAL* 1.3 61.4 + - - -
653B THR* 3.1 6.8 + - - -
654B TYR* 3.1 29.3 + - - +
368C LEU* 4.2 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B GLU* 3.8 16.2 - - + +
611B GLN* 3.5 28.3 - - + +
612B ARG* 4.1 12.9 - - + +
615B ALA* 4.7 3.5 - - + +
643B LEU* 3.6 43.1 - - + +
646B SER* 3.8 6.3 - - - +
648B ASN* 3.1 30.7 + - + +
650B GLY* 1.3 73.9 - - - +
652B ALA* 1.3 58.4 + - - +
654B TYR* 3.9 1.4 - - - +
655B ALA* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B LEU 3.6 12.3 + - - +
644B LEU* 3.7 21.3 - - - +
646B SER* 3.9 13.2 - - - +
648B ASN 3.0 9.4 + - - +
649B GLU* 3.5 10.5 - - - +
651B VAL* 1.3 79.6 - - - +
653B THR* 1.3 62.3 + - - +
655B ALA* 3.6 1.8 - - - +
656B ALA* 2.9 26.0 + - - +
364C GLN* 4.7 6.5 - - + +
397C GLY 4.7 8.5 - - - +
400C GLY* 5.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B GLU* 2.5 31.0 + - - -
650B GLY* 3.5 6.7 - - - -
652B ALA* 1.3 73.2 - - - +
654B TYR* 1.3 62.8 + - + +
656B ALA* 3.5 4.0 + - - +
657B ALA* 3.2 18.7 + - - +
329C ARG* 3.4 38.0 + - + +
361C GLY* 5.1 2.5 - - - +
364C GLN* 2.9 38.3 + - + +
365C ALA* 4.0 9.0 - - + +
368C LEU* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 3.3 38.3 + + - -
612B ARG* 3.7 24.8 + - + +
615B ALA* 3.6 21.3 - - + +
616B GLY* 3.5 15.7 - - - -
619B CYS* 3.9 21.1 - - + -
620B GLU* 5.5 1.5 + - + +
650B GLY 3.1 14.6 + - - +
651B VAL 4.9 0.2 - - - -
653B THR* 1.3 79.2 - - + +
655B ALA* 1.3 67.7 + - - +
657B ALA* 2.9 3.5 + - - +
658B VAL* 2.8 26.2 + - - +
326C ASN* 5.5 0.2 - - - -
329C ARG* 3.6 50.5 + - + -
330C THR* 3.7 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B ALA* 4.1 3.1 - - + +
640B LEU* 3.7 41.6 - - + +
643B LEU* 4.1 18.6 - - + -
644B LEU* 4.1 4.5 - - - +
651B VAL 2.8 18.6 + - - +
652B ALA 3.6 4.3 - - - +
654B TYR* 1.3 77.7 - - - +
656B ALA* 1.3 68.9 + - - +
658B VAL* 3.3 1.7 + - - +
659B LEU* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LEU* 3.6 17.3 - - + +
652B ALA 2.9 15.2 + - - +
653B THR 3.6 5.6 - - - +
655B ALA* 1.3 76.7 - - - +
657B ALA* 1.3 64.7 + - - +
659B LEU* 3.3 5.8 + - - +
660B PHE* 3.0 22.2 + - - +
360C ALA 5.4 0.9 - - - -
361C GLY* 4.8 8.5 - - - -
364C GLN* 3.3 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B CYS* 3.6 13.5 - - - -
653B THR 3.2 7.8 + - - +
654B TYR* 2.9 10.6 + - - +
656B ALA* 1.3 75.4 - - - +
658B VAL* 1.3 66.8 + - - +
660B PHE* 2.8 17.8 + - - +
661B ARG* 3.0 19.8 + - + +
329C ARG* 3.4 42.4 - - - +
360C ALA 4.8 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B ALA* 3.2 29.6 - - - +
618B LEU* 3.9 23.8 - - + +
619B CYS* 3.5 17.5 - - - +
622B ALA* 4.7 5.6 - - + +
631B ILE* 4.7 2.9 - - + -
640B LEU* 3.3 26.9 - - + -
654B TYR 2.8 17.2 + - - +
655B ALA 3.8 1.1 - - - +
657B ALA* 1.3 73.1 - - - +
659B LEU* 1.3 63.8 + - - +
661B ARG* 3.5 3.1 + - - +
662B MET* 3.0 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B THR* 4.1 28.3 - - + +
640B LEU* 3.4 32.8 - - + -
641B THR* 4.4 7.2 - - - +
644B LEU* 3.5 40.4 - - + -
655B ALA 3.2 10.6 + - - +
656B ALA* 3.5 6.7 - - - +
658B VAL* 1.3 78.8 - - - +
660B PHE* 1.3 65.0 + - - +
662B MET* 3.1 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ALA 3.0 12.4 + - - +
657B ALA* 2.8 13.0 + - - +
659B LEU* 1.3 74.2 - - - +
661B ARG* 1.3 73.3 + - + +
662B MET* 2.5 22.5 + - - -
322C GLN* 4.0 20.4 - - + -
329C ARG* 5.9 1.8 - - - -
356C ALA 5.3 1.1 - - - -
359C GLU* 3.0 48.0 - - + +
360C ALA* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B CYS* 2.9 35.8 + - - -
620B GLU* 4.3 2.0 + - - -
622B ALA* 3.4 27.2 - - + +
623B GLN* 3.1 40.9 - - - +
624B ASP 4.8 0.9 - - - +
628B ALA* 3.4 8.3 - - - +
657B ALA 3.0 16.4 + - - +
658B VAL* 3.7 4.0 - - - +
660B PHE* 1.3 82.7 - - + +
662B MET* 1.3 59.3 + - - +
322C GLN* 3.7 27.6 - - - +
326C ASN* 3.0 36.5 - - - +
329C ARG* 3.8 7.9 - - - +
----------------------------------------------------------
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