Contacts of the helix formed by residues 871 - 883 (chain L) in PDB entry 6KW5
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 SER 871 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 4.0 1.6 - - - +
134A GLU* 3.3 12.6 - - - -
137A ARG* 6.3 0.9 - - - -
322D LEU* 4.4 12.2 - - - +
325D GLU* 2.3 40.1 + - - +
340D HIS* 3.7 14.8 + - - -
869L ARG 3.9 0.8 + - - -
870L PRO* 1.3 77.0 - - - +
872L ALA* 1.3 63.7 + - - +
873L LYS* 3.4 7.0 + - - +
874L PHE* 3.5 5.9 + - - +
875L THR* 3.4 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 872 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.8 18.1 - - - +
17A VAL* 5.2 1.3 - - + -
20A ILE* 3.5 26.8 - - + +
130A LEU* 5.1 11.7 - - + -
133A ARG* 4.6 1.8 - - - +
134A GLU* 2.5 30.6 + - - +
870L PRO 4.0 0.4 + - - -
871L SER* 1.3 71.3 - - - +
873L LYS* 1.3 59.8 + - - +
874L PHE 3.3 0.2 - - - -
875L THR* 3.2 3.9 + - - -
876L ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 873 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 4.3 21.5 - - - +
16A ASN* 4.1 10.6 - - - +
329D MET* 4.1 11.7 - - + -
330D TYR* 2.9 37.2 + - + +
336D LYS* 6.0 1.8 - - - +
340D HIS* 5.1 6.3 - - + +
871L SER* 3.3 7.2 + - - +
872L ALA* 1.3 78.7 - - - +
874L PHE* 1.3 57.1 + - - +
876L ALA* 3.5 5.4 + - + +
877L HIS* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 874 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ARG* 5.4 0.2 - - - -
325D GLU* 3.2 43.6 + - + +
328D GLU* 3.6 33.9 - - + -
329D MET* 3.7 28.4 - - + +
218J LEU* 3.4 45.8 - - + -
221J CYS* 3.6 23.6 - - + -
870L PRO* 5.3 4.9 - - + -
871L SER 3.5 4.4 + - - +
872L ALA 3.3 0.4 - - - -
873L LYS* 1.3 76.8 - - - +
875L THR* 1.3 60.4 + - - +
877L HIS* 3.5 4.7 - - + +
878L ARG* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 875 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.7 25.8 - - + -
126A PHE* 6.3 0.7 - - + -
221J CYS* 3.7 38.5 - - + +
222J LEU* 5.7 0.4 - - + -
224J PHE* 4.5 8.7 - - + -
870L PRO* 4.7 7.1 - - - +
871L SER 3.4 11.9 + - - -
872L ALA* 3.2 9.8 + - - -
874L PHE* 1.3 79.8 - - - +
876L ALA* 1.3 58.7 + - - +
878L ARG* 3.3 5.9 + - - +
879L LEU* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 876 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 5.6 1.3 - - - +
16A ASN* 3.7 19.1 - - + +
19A SER* 3.6 25.6 + - - +
20A ILE* 4.2 2.3 - - - +
872L ALA 2.9 16.2 + - - +
873L LYS* 3.8 5.2 - - + +
875L THR* 1.3 74.6 - - - +
877L HIS* 1.3 59.2 + - - +
879L LEU* 3.7 4.0 - - - +
880L SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 877 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D GLU* 4.7 5.6 - - + +
329D MET* 3.6 49.0 + - + +
873L LYS 2.9 19.2 + - - +
874L PHE* 3.5 9.7 - - - +
876L ALA* 1.3 76.5 - - - +
878L ARG* 1.3 58.6 + - - +
880L SER* 2.4 28.1 + - - -
881L MET* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 878 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ARG* 3.1 20.0 - - - +
218J LEU 3.3 13.5 + - - -
219J ASP* 2.4 40.0 + - - +
221J CYS* 4.0 13.0 - - - -
222J LEU* 3.7 39.4 - - + +
874L PHE* 2.9 26.2 + - + +
875L THR 3.8 3.4 - - - +
876L ALA 3.3 0.2 - - - -
877L HIS* 1.3 75.1 + - - +
879L LEU* 1.3 61.1 + - - +
881L MET* 3.2 27.2 + - - +
882L LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 879 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.9 9.2 - - - +
20A ILE* 3.9 30.1 - - + +
23A ALA* 3.8 33.2 - - + -
222J LEU* 3.8 23.3 - - + -
224J PHE* 4.7 10.8 - - + -
875L THR* 2.9 25.9 + - + +
876L ALA* 3.9 4.7 - - - +
877L HIS 3.4 0.2 - - - -
878L ARG* 1.3 74.1 - - - +
880L SER* 1.3 62.4 + - - +
882L LEU* 3.3 33.0 + - + +
883L ARG 3.9 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 880 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876L ALA 2.9 13.1 + - - -
877L HIS* 2.4 36.1 + - - -
879L LEU* 1.3 76.6 - - - +
881L MET* 1.3 59.5 + - - +
882L LEU 3.1 0.6 + - - -
883L ARG 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 881 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D GLU* 4.9 15.0 - - - +
877L HIS* 2.9 47.4 + - + +
878L ARG* 3.2 30.2 + - - +
880L SER* 1.3 76.4 + - - +
882L LEU* 1.3 64.3 + - - +
883L ARG* 4.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 882 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 6.2 0.2 - - + -
222J LEU* 4.6 14.1 - - + -
878L ARG 2.9 11.0 + - - +
879L LEU* 3.3 36.1 - - + +
880L SER 3.1 0.6 - - - -
881L MET* 1.3 78.7 - - - +
883L ARG* 1.3 80.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 883 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879L LEU 3.9 3.3 + - - -
880L SER* 3.0 20.2 + - - +
881L MET 4.6 1.1 - - - -
882L LEU* 1.3 97.4 + - + +
----------------------------------------------------------
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