Contacts of the helix formed by residues 75 - 87 (chain A) in PDB entry 1C7G
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 GLU 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.0 23.5 + - + +
73A GLY 4.9 0.4 - - - +
74A SER* 1.3 70.9 + - - +
76A ASN* 1.3 67.3 + - - +
78A TYR* 3.3 28.4 + - - +
79A HIS* 3.1 48.3 + - + -
39C ASN* 5.1 0.2 - - - -
41C LYS* 3.1 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.6 17.8 + - - +
67A GLY* 3.4 0.8 - - - -
68A ASP* 2.6 32.9 + - - +
74A SER* 3.2 4.2 - - - +
75A GLU* 1.3 80.6 - - - +
77A PHE* 1.3 56.8 + - - +
79A HIS* 3.4 5.8 + - - +
80A LEU* 3.0 26.2 + - - +
296A GLY* 3.0 38.3 - - - +
299A MET* 4.0 8.6 - - + +
300A GLU* 2.7 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 6.0 1.1 - - - -
74A SER* 3.3 14.9 + - - +
75A GLU 3.2 0.6 - - - -
76A ASN* 1.3 77.3 - - - +
78A TYR* 1.3 75.2 + + - +
80A LEU* 3.1 5.6 + - + -
81A GLU* 2.7 71.1 + - + +
93A ILE* 4.5 14.6 - - + -
95A PRO* 3.8 17.5 - - + -
289A PRO 3.8 20.0 - - - -
290A SER* 3.7 34.5 - - - +
299A MET* 4.0 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY* 3.3 37.0 - - - -
74A SER 3.4 9.6 - - - -
75A GLU* 3.3 28.9 + - - +
77A PHE* 1.3 97.6 - + - +
79A HIS* 1.3 63.5 + - + +
81A GLU* 3.7 14.7 - - - +
82A LYS* 2.9 33.3 + - - +
37C LEU 5.0 2.6 + - - -
38C LEU 4.5 1.4 + - - -
39C ASN* 2.6 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 5.4 6.7 - - + -
75A GLU* 3.1 39.6 + - + -
76A ASN* 3.4 9.2 - - - +
77A PHE 3.1 0.2 - - - -
78A TYR* 1.3 80.0 - - + +
80A LEU* 1.3 60.7 + - - +
82A LYS* 3.9 6.8 - - + +
83A THR* 2.9 30.4 + - - -
300A GLU* 2.6 39.8 + - - +
303A ALA* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN 3.0 13.6 + - - +
77A PHE* 3.7 9.2 - - + +
79A HIS* 1.3 74.6 - - - +
81A GLU* 1.3 67.2 + - - +
83A THR* 3.4 0.7 + - - -
84A VAL* 3.0 40.5 + - + +
93A ILE* 4.0 17.7 - - + -
95A PRO* 4.4 14.6 - - + -
266A PHE* 4.7 3.8 - - + -
299A MET* 3.8 27.8 - - + +
302A MET* 3.8 33.9 - - + +
303A ALA* 3.7 29.3 - - - +
306A LEU* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 2.7 48.1 + - + +
78A TYR* 3.7 15.9 - - - +
80A LEU* 1.3 75.4 - - - +
82A LYS* 1.3 56.8 + - - +
84A VAL* 4.0 1.2 - - - +
85A LYS* 3.0 68.1 + - - +
93A ILE* 3.8 24.5 + - + +
275A PHE* 6.1 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR 2.9 17.6 + - - +
79A HIS* 3.9 7.4 - - + +
81A GLU* 1.3 79.7 - - - +
83A THR* 1.3 58.5 + - - +
85A LYS* 3.5 6.4 + - - +
86A GLU* 2.9 58.1 + - - +
307A ARG* 4.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 2.9 22.5 + - - +
80A LEU 3.8 3.1 - - - -
82A LYS* 1.3 77.1 - - - +
84A VAL* 1.3 57.8 + - - +
86A GLU* 3.1 2.4 + - - +
87A LEU* 2.8 48.5 + - + +
303A ALA* 3.6 31.7 + - - +
306A LEU* 4.2 10.8 - - + -
307A ARG* 3.4 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.0 25.8 + - + +
81A GLU 4.2 0.9 - - - +
83A THR* 1.3 74.6 - - - +
85A LYS* 1.3 60.4 + - + +
87A LEU 4.5 0.2 - - - +
88A PHE* 2.8 41.3 + - + +
89A GLY 3.5 0.3 + - - -
90A PHE* 4.5 2.4 + - + -
93A ILE* 3.8 21.1 - - + -
266A PHE* 3.6 30.7 - - + -
268A CYS* 3.6 31.0 - - - -
306A LEU* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.0 51.4 + - - +
82A LYS* 3.8 6.3 - - - +
84A VAL* 1.3 77.7 - - + +
86A GLU* 1.3 63.9 + - - +
89A GLY* 3.2 21.3 + - - -
90A PHE 3.4 20.1 - - - +
91A LYS* 2.8 30.2 + - - +
92A HIS* 4.2 7.6 + - - +
93A ILE* 4.6 5.8 - - + +
242A HIS* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 2.9 37.4 + - + +
83A THR 3.1 4.2 + - - +
85A LYS* 1.3 80.2 - - - +
87A LEU* 1.3 67.4 + - + +
238A LYS* 4.5 13.8 + - + +
242A HIS* 3.7 16.3 + - - -
307A ARG* 2.8 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 2.8 39.2 + - + +
84A VAL* 5.0 0.7 - - - -
86A GLU* 1.3 85.6 - - + +
88A PHE* 1.3 74.5 + - + +
238A LYS* 3.6 39.9 - - + +
241A VAL* 3.9 6.2 - - + +
242A HIS* 3.6 23.4 + - - +
306A LEU* 3.9 22.2 - - + +
307A ARG* 4.3 18.2 - - + +
310A MET* 4.0 24.0 - - + -
----------------------------------------------------------
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