Contacts of the helix formed by residues 651 - 664 (chain A) in PDB entry 3CMM
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 VAL 651 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A THR* 4.1 23.5 - - + +
645A LEU* 4.9 24.0 - - + +
650A ASP* 1.3 97.2 - - - +
652A LYS* 1.3 67.2 + - - +
653A GLY 3.5 1.1 - - - +
654A VAL* 3.6 5.0 + - - +
655A LEU* 3.5 32.2 + - + +
798A ILE* 6.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ASP 4.8 0.4 - - - +
651A VAL* 1.3 80.9 - - - +
653A GLY* 1.3 69.4 + - - +
655A LEU* 3.4 8.7 + - - +
656A GLU* 3.1 67.2 + - - +
798A ILE* 6.1 6.7 - - + -
801A LEU* 4.2 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ASP 5.0 4.0 - - - +
651A VAL 3.5 2.4 - - - +
652A LYS* 1.3 88.7 - - - +
654A VAL* 1.3 65.6 + - - +
656A GLU* 3.8 7.4 - - - +
657A SER* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ASN* 4.6 17.3 + - - +
640A PHE* 4.4 11.7 - - + -
644A THR* 3.8 22.9 - - + -
650A ASP* 3.3 33.6 - - + +
651A VAL 3.6 8.4 + - - +
652A LYS 3.3 0.6 - - - -
653A GLY* 1.3 78.5 - - - +
655A LEU* 1.3 63.2 + - + +
657A SER* 3.2 16.9 - - - -
658A ILE* 3.5 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A PHE* 5.8 1.3 - - + -
641A VAL* 4.3 17.9 - - + +
644A THR* 5.1 15.3 - - + +
645A LEU* 5.5 8.1 - - + -
651A VAL* 3.5 23.3 + - + +
652A LYS* 3.4 9.5 + - - +
653A GLY 3.3 0.4 - - - -
654A VAL* 1.3 77.6 - - + +
656A GLU* 1.3 59.3 + - - +
658A ILE* 2.9 30.3 + - + +
659A SER* 3.1 13.4 + - - -
798A ILE* 4.7 9.2 - - + +
801A LEU* 4.7 18.4 - - + +
802A VAL* 4.1 24.2 - - + +
805A LEU* 4.2 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A LYS* 3.1 58.5 + - - +
653A GLY* 3.8 6.6 - - - +
655A LEU* 1.3 74.3 - - - +
657A SER* 1.3 58.3 + - - +
659A SER* 4.0 7.2 - - - -
660A ASP* 3.0 47.2 + - - +
801A LEU* 3.9 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A SER* 4.3 19.0 + - - +
630A ASN* 4.5 15.2 + - - -
631A VAL* 4.1 2.4 - - - +
653A GLY 3.0 14.6 + - - -
654A VAL* 3.2 14.3 - - - -
656A GLU* 1.3 75.8 - - - +
658A ILE* 1.3 57.7 + - - +
660A ASP* 5.0 4.3 - - - -
661A SER* 2.8 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ASN* 3.8 30.3 - - + +
631A VAL* 4.1 9.0 - - + +
634A TYR* 3.6 36.1 - - + -
640A PHE* 3.6 31.4 - - + -
654A VAL* 3.5 20.9 - - + +
655A LEU* 2.9 17.2 + - + +
657A SER* 1.3 79.8 - - - +
659A SER* 1.3 60.4 + - - +
662A LEU* 3.1 29.1 - - + +
805A LEU* 3.9 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A LEU 3.1 7.8 + - - -
656A GLU* 3.6 10.9 + - - -
658A ILE* 1.3 77.2 - - - +
660A ASP* 1.3 73.9 + - - +
661A SER 3.3 0.4 - - - -
662A LEU* 3.6 2.6 - - - +
663A SER* 2.9 29.8 + - - -
801A LEU* 4.6 13.3 - - - +
804A SER* 4.8 12.6 - - - -
805A LEU* 3.7 19.5 - - - -
806A PRO* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLU* 3.0 26.7 + - - +
657A SER* 4.9 2.7 - - - +
659A SER* 1.3 80.5 + - - +
661A SER* 1.3 55.9 + - - +
662A LEU 2.7 12.1 + - - -
663A SER* 4.4 3.4 - - - -
664A SER* 2.9 35.2 + - - -
738A ARG* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A SER* 3.8 20.1 + - - -
631A VAL* 3.7 18.6 - - - -
657A SER* 2.8 26.3 + - - -
658A ILE* 4.4 0.2 - - - -
659A SER 3.3 0.2 - - - -
660A ASP* 1.3 78.7 - - - +
662A LEU* 1.3 67.2 + - - +
664A SER* 4.7 1.3 - - - -
665A LYS* 4.3 0.5 - - - +
738A ARG* 5.1 5.7 + - - +
742A TYR* 2.8 36.5 + - - -
816A LEU* 4.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A VAL* 3.8 27.4 - - + -
634A TYR* 4.1 27.6 - - + -
635A LEU* 5.0 2.5 - - + -
658A ILE* 3.1 27.8 - - + +
659A SER* 3.1 6.1 + - - +
660A ASP 2.7 7.1 + - - -
661A SER* 1.3 83.3 - - - +
663A SER* 1.3 57.5 + - - +
664A SER 3.5 1.1 - - - -
665A LYS* 3.3 27.4 + - - +
806A PRO* 4.5 18.4 - - + +
811A LEU* 3.8 32.9 - - + +
814A PHE* 4.3 17.3 - - + -
816A LEU* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A SER* 2.9 20.4 + - - -
660A ASP* 4.0 2.9 + - - -
662A LEU* 1.3 76.8 - - - +
664A SER* 1.3 57.7 + - - +
665A LYS* 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ASP* 2.9 25.2 + - - -
663A SER* 1.3 81.0 - - - +
665A LYS* 1.3 63.6 + - - +
666A PRO* 3.2 2.6 - - - +
675A TRP* 4.4 11.6 + - - -
738A ARG* 3.1 27.3 + - - -
742A TYR* 4.8 0.2 - - - -
----------------------------------------------------------
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