Contacts of the helix formed by residues 78 - 89 (chain A) in PDB entry 6ICV
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 TYR 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.6 18.0 - + + +
72A ASP* 3.5 11.6 + - - +
73A GLY* 2.8 38.8 + - - -
74A LYS 3.3 25.1 - - - -
75A ARG* 3.0 4.2 + - - +
76A GLU 3.0 1.2 - - - -
77A ASP* 1.3 82.1 - - + +
79A PHE* 1.3 63.4 + - - +
80A PRO* 3.3 2.7 - - - -
81A ASP* 3.2 23.2 + - + +
82A LEU 3.1 16.5 + - - -
174A PRO* 4.5 1.2 - - + +
177A GLN* 3.5 51.4 + - + +
178A THR* 3.3 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.7 20.4 + - + -
76A GLU* 3.2 30.5 + - + +
78A TYR* 1.3 77.6 - - - +
80A PRO* 1.3 69.1 - - + +
82A LEU* 3.1 19.1 + - + +
83A MET* 3.0 27.3 + - - +
98A MET* 3.7 43.5 - - + -
106A PHE* 3.5 35.9 - + - -
178A THR* 3.6 29.1 - - + +
276A MET* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU 3.6 10.3 - - - +
77A ASP* 3.6 10.8 - - - +
78A TYR 3.5 3.8 - - - -
79A PHE* 1.3 93.8 - - + +
81A ASP* 1.3 59.6 + - - +
83A MET* 3.4 8.0 + - + +
84A LYS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP 4.7 2.9 - - - +
78A TYR* 3.2 32.4 + - + +
80A PRO* 1.3 77.5 - - - +
82A LEU* 1.3 66.3 + - - +
84A LYS* 4.0 7.6 - - - +
85A TRP* 2.9 27.9 + - - +
174A PRO* 3.7 17.3 - - + +
177A GLN* 4.9 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR 3.1 9.4 + - - +
79A PHE* 3.1 29.3 + - + +
81A ASP* 1.3 76.5 - - - +
83A MET* 1.3 57.3 + - - +
85A TRP* 3.8 22.2 - - + +
86A ALA* 2.9 33.3 + - + +
98A MET* 5.1 3.6 - - + -
174A PRO* 3.9 24.8 - - - +
175A TYR* 4.0 13.0 - - + -
178A THR* 3.7 16.4 - - + +
272A PRO* 4.5 9.9 - - + -
273A LEU* 4.5 32.3 - - + +
276A MET* 5.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE 3.0 16.6 + - - +
80A PRO* 3.8 8.1 - - + +
82A LEU* 1.3 76.6 - - - +
84A LYS* 1.3 59.2 + - - +
86A ALA* 4.6 0.4 - - - -
87A SER* 2.8 31.9 + - - -
93A VAL* 3.4 42.2 - - + +
96A PHE* 3.8 27.6 - - + +
97A GLU* 5.7 0.4 - - - -
98A MET* 3.6 27.1 - - + -
273A LEU* 3.8 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO 3.0 15.9 + - - +
81A ASP* 4.0 8.1 - - - +
83A MET* 1.3 76.6 - - - +
85A TRP* 1.3 63.1 + - - +
87A SER* 3.6 5.5 - - - -
88A GLU* 2.5 71.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP 2.9 18.9 + - - +
82A LEU* 3.8 12.6 - - + +
84A LYS* 1.3 79.5 - - - +
86A ALA* 1.3 71.6 + - + +
88A GLU* 3.3 10.2 + - - +
89A ASN* 2.9 39.9 + - - -
127A LEU* 3.5 41.3 - - + -
171A PHE* 3.0 58.9 + + - -
172A TRP* 3.8 14.8 - + - -
174A PRO* 3.6 26.9 - - + -
175A TYR* 3.8 24.2 - - + -
272A PRO* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.9 19.9 + - + +
83A MET 3.9 2.7 - - - +
85A TRP* 1.3 81.1 - - + +
87A SER* 1.3 61.0 + - - +
89A ASN 3.2 8.5 + - - -
90A GLY 3.2 0.3 + - - -
91A ALA* 2.9 42.0 + - + +
93A VAL* 4.1 7.9 - - + -
127A LEU* 3.8 18.1 - - + +
272A PRO* 6.2 0.4 - - + -
273A LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET 2.8 20.8 + - - -
84A LYS* 3.6 7.2 - - - -
86A ALA* 1.3 77.0 - - - +
88A GLU* 1.3 62.9 + - - +
90A GLY* 3.1 13.9 + - - -
91A ALA 4.0 6.8 + - - +
93A VAL* 3.7 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 2.5 57.1 + - + +
85A TRP* 3.3 12.1 + - - +
87A SER* 1.3 76.1 - - - +
89A ASN* 1.3 65.7 + - - +
90A GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TRP* 2.9 39.7 + - - +
86A ALA 3.2 2.3 + - - +
87A SER 3.1 1.0 - - - -
88A GLU* 1.3 85.8 + - - +
90A GLY* 1.3 58.1 + - - +
91A ALA 3.5 2.7 - - - -
124A PRO* 3.2 23.2 - - - +
126A LYS* 3.3 38.4 + - + +
127A LEU* 3.6 26.3 - - + +
171A PHE* 3.8 12.8 - - - -
----------------------------------------------------------
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