Contacts of the helix formed by residues 653 - 670 (chain B) in PDB entry 4N41
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 PRO 653 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 4.0 23.6 - - + -
573B VAL* 4.6 4.7 - - + -
617B LEU* 4.3 7.6 - - + -
635B ILE* 3.7 38.4 - - + +
638B LEU* 3.9 9.4 - - + -
639B THR* 3.9 12.5 - - + +
651B ARG 4.3 3.1 - - - +
652B LEU* 1.3 94.9 - - + +
654B ALA* 1.3 66.0 + - - +
655B PRO* 3.3 1.8 - - + -
656B LEU* 3.0 28.7 + - + -
657B HIS 3.2 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B VAL* 4.6 4.9 - - + -
501B LEU* 5.9 0.9 - - + -
638B LEU* 3.1 23.2 + - - +
639B THR* 5.2 0.9 - - - +
641B LEU* 3.9 18.6 - - + -
642B TYR* 4.1 18.6 - - + +
650B PRO* 6.1 0.2 - - - -
652B LEU 3.4 3.8 + - - -
653B PRO* 1.3 70.7 - - - +
655B PRO* 1.3 71.2 - - + +
657B HIS* 3.7 6.9 - - - +
658B LEU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B ALA* 3.6 27.4 - - + +
475B VAL 4.1 0.7 - - - -
476B GLY* 3.5 26.8 - - - +
492B CYS* 3.5 19.8 - - + +
494B VAL* 3.8 16.2 - - + -
544B LEU* 4.6 7.6 - - + -
638B LEU* 4.3 8.5 - - + -
653B PRO* 3.4 11.9 - - + -
654B ALA* 1.3 94.0 - - + +
656B LEU* 1.3 56.7 + - - +
658B LEU* 4.5 3.6 - - + -
659B ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B GLY* 3.7 9.2 - - - -
477B PHE 3.9 14.6 - - - +
478B ASP* 4.8 4.3 - - - +
544B LEU* 3.5 38.8 - - + +
545B ARG* 4.1 10.1 - - - +
546B ASP* 4.7 2.2 - - + +
573B VAL* 3.8 35.9 - - + +
652B LEU* 4.4 18.0 - - + +
653B PRO* 3.0 23.7 + - + +
655B PRO* 1.3 77.2 - - - +
657B HIS* 1.3 61.2 + - - +
659B ALA* 3.7 3.1 - - + +
660B ASP* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TYR* 3.4 39.2 - + + -
650B PRO* 3.8 22.7 - - + +
652B LEU* 4.2 23.6 - - + +
653B PRO 3.2 11.8 + - - +
654B ALA* 3.3 11.6 + - - +
656B LEU* 1.3 77.2 - - - +
658B LEU* 1.3 61.9 + - - +
660B ASP* 3.4 6.9 + - - +
661B ARG* 3.1 40.7 + - + +
4E G 2.5 29.1 + - - -
5E G 4.3 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B CYS* 3.5 25.1 - - + -
493B ALA 5.3 2.5 - - - +
494B VAL* 5.1 2.7 - - + -
501B LEU* 4.4 28.3 - - + -
502B LEU 5.7 1.3 - - - +
642B TYR* 3.6 28.7 - - + -
643B PRO* 4.9 0.7 - - + -
654B ALA* 2.9 30.8 + - + +
655B PRO* 4.5 1.6 - - + -
657B HIS* 1.3 75.3 - - - +
659B ALA* 1.3 59.3 + - - +
661B ARG* 3.3 2.5 + - - -
662B LEU* 2.9 26.9 + - - +
682B LEU* 4.1 16.6 - - + -
684B PHE* 3.3 27.9 - - + -
685B VAL* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B GLY 3.7 19.5 - - - +
477B PHE 4.6 0.2 - - - -
478B ASP* 3.6 22.4 - - + +
490B ALA 4.7 0.2 - - - +
491B ALA* 4.6 3.6 - - - +
492B CYS* 3.4 14.3 - - - +
655B PRO 2.9 19.8 + - - +
656B LEU* 3.3 7.6 + - - +
658B LEU* 1.3 74.9 - - - +
660B ASP* 1.3 58.2 + - - +
662B LEU* 3.4 3.6 + - - +
663B VAL* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ASP* 2.9 11.0 - - - +
575B LYS* 3.9 17.9 + - - -
652B LEU* 5.4 4.2 - - + +
656B LEU 2.9 16.4 + - - +
657B HIS* 3.4 9.2 - - - +
659B ALA* 1.3 76.6 - - - +
661B ARG* 1.3 65.0 + - + +
663B VAL* 3.2 4.3 + - - +
664B LYS* 3.0 54.0 + - - +
701B MG 2.2 31.2 - - - -
6F T 3.1 9.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
642B TYR* 3.4 23.0 + - - +
657B HIS* 3.1 32.9 + - + +
658B LEU* 3.9 4.0 - - - +
660B ASP* 1.3 77.4 - - + +
662B LEU* 1.3 57.2 + - - +
664B LYS* 3.4 25.7 + - + +
665B GLU* 3.0 34.0 + - - +
668B ARG* 6.2 0.4 - - - +
684B PHE* 4.0 19.1 - - + +
685B VAL* 4.1 16.9 + - - -
3E A 4.3 13.5 + - - -
4E G 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ALA* 3.8 21.5 - - + -
491B ALA 3.7 22.7 - - - +
492B CYS* 3.8 8.5 - - - -
503B TRP* 3.9 11.7 - - + -
504B THR 4.2 5.6 - - - +
505B LEU* 4.2 10.5 - - + -
658B LEU 2.9 17.5 + - - +
659B ALA 3.5 4.0 - - - +
661B ARG* 1.3 74.2 - - - +
663B VAL* 1.3 61.3 + - - +
665B GLU* 3.2 2.1 + - - +
666B VAL* 2.9 42.0 + - + +
683B PHE* 3.7 20.0 - - + -
684B PHE* 3.5 35.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ASP* 3.4 33.2 - - + +
479B ALA 5.2 0.2 - - - -
480B GLY* 4.5 17.5 - - - +
482B ARG* 5.7 2.9 - - - +
489B GLY* 4.9 2.2 - - - -
490B ALA* 3.7 24.5 - - + +
659B ALA 2.9 20.5 + - - +
660B ASP 3.7 3.4 - - - +
662B LEU* 1.3 75.2 - - - +
664B LYS* 1.3 65.1 + - + +
666B VAL* 3.2 10.3 + - + +
667B GLY* 2.9 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B ASP* 3.0 42.9 + - - +
661B ARG* 3.5 30.5 - - - +
662B LEU 3.3 0.2 - - - -
663B VAL* 1.3 78.3 - - + +
665B GLU* 1.3 57.7 + - + +
667B GLY* 3.2 3.5 + - - -
668B ARG* 3.0 55.9 + - - +
7F A 2.9 43.1 + - - +
8F C 6.0 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
418B ARG* 3.1 31.9 + - - -
422B LYS* 4.8 2.6 - - - -
661B ARG* 3.0 15.8 + - + +
662B LEU 3.8 1.1 - - - +
664B LYS* 1.3 75.7 - - + +
666B VAL* 1.3 61.2 + - - +
668B ARG* 2.4 37.4 + - - +
669B LEU* 2.9 55.9 + - + +
683B PHE* 5.2 4.9 - - + -
684B PHE* 3.3 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ALA* 5.8 0.2 - - + -
505B LEU* 3.6 36.1 - - + -
662B LEU* 2.9 26.6 + - + +
663B VAL* 3.5 12.1 - - + +
665B GLU* 1.3 77.0 - - - +
667B GLY* 1.3 58.9 + - - +
669B LEU* 5.0 1.6 - - - -
670B GLY* 2.9 30.8 + - - +
671B ILE* 3.7 34.4 + - + +
683B PHE* 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B VAL 2.9 13.8 + - - -
664B LYS* 3.6 4.0 - - - -
666B VAL* 1.3 79.0 - - - +
668B ARG* 1.3 61.2 + - - +
669B LEU 3.6 0.2 + - - -
670B GLY* 4.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TRP* 3.4 45.9 - - + +
418B ARG* 3.8 16.2 - - - +
419B ASN* 3.7 24.8 + - - +
661B ARG* 6.2 0.2 - - - +
664B LYS* 3.0 43.4 + - - +
665B GLU* 2.4 39.2 + - - +
667B GLY* 1.3 79.4 - - - +
669B LEU* 1.3 63.8 + - + +
1E T 5.5 3.8 - - - -
8F C 5.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 4.3 3.6 - - - +
419B ASN* 3.5 38.4 - - + +
422B LYS* 4.1 21.3 - - + +
423B ALA* 4.2 20.1 - - + +
426B LEU* 3.8 28.9 - - + -
427B ARG* 5.8 0.5 + - - -
665B GLU* 2.9 37.1 + - + +
666B VAL* 5.0 0.9 - - - -
668B ARG* 1.3 88.0 - - - +
670B GLY* 1.3 67.2 + - - +
683B PHE* 5.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B LEU* 6.1 1.2 - - - +
666B VAL* 2.9 14.5 + - - -
667B GLY 4.4 2.9 + - - -
668B ARG 3.8 0.6 - - - -
669B LEU* 1.3 84.1 - - - +
671B ILE* 1.3 64.0 + - - -
----------------------------------------------------------
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