Contacts of the helix formed by residues 695 - 704 (chain B) in PDB entry 6CNB
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 GLN 695 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A PHE* 4.3 0.4 - - + -
864A HIS* 3.2 22.6 + - + +
694B ASN* 1.3 75.8 - - - +
696B SER* 1.3 65.3 + - - +
697B PRO* 3.3 12.0 - - + +
698B ARG* 2.9 50.6 + - + +
699B ASN 4.1 0.2 + - - -
951B SER 4.6 2.8 + - - -
952B ARG* 2.9 30.8 + - - +
953B MET* 3.1 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A PHE* 5.4 9.6 - - - -
864A HIS* 2.9 26.5 + - - -
865A ALA* 3.3 31.4 + - - -
868A GLY* 4.9 1.9 - - - -
869A ARG* 4.6 6.1 - - - +
499B THR 6.0 1.6 - - - -
500B ALA* 5.9 0.5 - - - -
694B ASN 4.1 0.6 + - - -
695B GLN* 1.3 70.6 - - - +
697B PRO* 1.3 76.5 - - - +
699B ASN* 2.8 26.1 + - - +
700B THR* 2.9 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A HIS* 5.1 1.1 - - + +
868A GLY* 4.2 30.3 - - - +
869A ARG* 4.9 4.7 - - - +
872A LEU* 5.4 9.0 - - + -
695B GLN* 3.3 17.0 - - + +
696B SER* 1.3 97.4 - - - +
698B ARG* 1.3 70.4 + - - +
700B THR* 3.2 10.3 + - - +
701B TYR* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B ASN* 4.8 9.0 - - + +
695B GLN* 2.9 38.0 + - + +
697B PRO* 1.3 86.1 - - - +
699B ASN* 1.3 57.3 + - - +
701B TYR* 3.4 32.6 + - - +
702B GLN* 2.9 27.6 + - - +
916B HIS 4.1 14.6 - - - +
917B GLY* 3.9 23.8 - - - -
951B SER 4.7 1.0 + - - -
952B ARG* 3.1 58.5 - - - +
954B THR* 4.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A PHE* 5.3 8.1 - - + -
500B ALA* 3.1 23.1 - - + +
681B LEU* 5.2 2.6 - - - +
688B ILE* 3.2 38.5 - - + +
691B PRO* 3.9 17.4 + - - +
694B ASN* 3.4 31.3 - - - +
696B SER* 2.8 20.8 + - - +
698B ARG* 1.3 73.7 - - - +
700B THR* 1.3 58.0 + - - +
702B GLN* 3.1 6.3 + - - +
703B CYS* 2.8 28.1 + - - -
916B HIS 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A ARG* 4.0 23.5 + - - +
872A LEU* 5.1 11.7 - - + -
499B THR 4.7 1.2 + - - -
500B ALA* 2.9 16.7 + - - -
501B ASP* 4.6 1.0 - - - +
502B THR* 3.8 32.1 - - - +
503B PRO* 5.1 3.4 - - + -
696B SER* 2.9 13.9 + - - -
697B PRO* 3.5 14.0 - - - +
698B ARG 3.2 0.2 - - - -
699B ASN* 1.3 73.7 - - - +
701B TYR* 1.3 71.3 + - + +
702B GLN 3.1 0.2 + - - -
703B CYS* 3.2 4.2 + - - +
704B ALA* 2.9 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LEU* 4.5 22.3 - - + +
504B GLU* 6.1 5.2 - - + -
697B PRO* 2.9 27.7 + - + +
698B ARG* 3.8 29.6 - - - +
700B THR* 1.3 78.5 - - + +
702B GLN* 1.3 56.9 + - - +
704B ALA* 3.2 11.4 + - + +
705B MET* 2.9 42.9 + - + +
917B GLY 5.0 5.8 - - - +
919B LYS* 5.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B VAL* 4.8 1.4 - - + +
687B LEU* 5.2 9.2 - - + +
688B ILE* 3.5 22.9 - - + -
698B ARG 2.9 17.7 + - - +
699B ASN* 3.4 9.6 - - - +
700B THR 3.0 0.6 - - - -
701B TYR* 1.3 73.6 - - - +
703B CYS* 1.3 57.6 + - - +
704B ALA 3.0 4.7 - - - -
705B MET* 2.9 30.0 + - - +
706B GLY* 2.9 30.9 + - - +
913B SER* 3.8 1.4 + - - -
915B ARG* 2.8 43.3 - - - +
916B HIS 4.8 0.9 - - - -
917B GLY 3.7 4.7 + - - +
1025B GLN* 3.6 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B CYS* 4.8 0.7 - - - -
500B ALA* 3.3 21.3 - - - +
501B ASP* 3.1 31.0 - - + +
503B PRO* 6.1 0.3 - - - +
684B VAL* 3.6 18.8 - - + +
685B ALA* 3.5 44.2 - - - -
688B ILE* 4.6 2.9 - - - -
699B ASN 2.8 15.2 + - - -
700B THR 3.9 0.2 - - - +
702B GLN* 1.3 72.9 - - - +
704B ALA* 1.3 57.1 + - - +
705B MET 3.3 0.2 - - - -
706B GLY 4.7 0.4 + - - -
707B LYS* 3.4 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ASP* 4.9 0.6 - - + +
503B PRO* 4.4 25.4 - - + -
700B THR* 2.9 13.8 + - + +
701B TYR* 3.3 18.8 - - + +
702B GLN 3.0 0.4 - - - -
703B CYS* 1.3 78.5 - - - +
705B MET* 1.3 60.3 + - + +
707B LYS* 4.6 9.6 - - - +
708B GLN* 4.5 10.9 - - - +
----------------------------------------------------------
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