Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 3C6G
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 LEU 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER 4.1 1.3 + - - +
60A GLU* 1.3 74.8 + - - +
62A PRO* 1.4 59.9 - - + +
63A HIS* 3.3 26.5 - - + +
64A VAL* 2.9 15.7 + - + +
65A TYR* 2.8 30.3 + - - +
482A LYS* 6.3 0.4 - - + -
483A PRO* 3.5 40.2 - - + +
484A ARG 4.8 0.7 - - - -
485A LEU* 3.9 42.0 - - + +
489A LEU* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.8 30.2 - - + +
60A GLU 3.8 1.8 - - - +
61A LEU* 1.4 89.6 - - + +
63A HIS* 1.3 60.0 + - - +
65A TYR* 3.4 3.8 - - + +
66A MET* 2.9 37.8 + - - +
222A ALA* 5.6 2.7 - - + +
227A PHE* 6.2 5.4 - - + -
377A LEU* 4.3 16.2 - - + -
485A LEU* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.7 27.5 - - + +
62A PRO* 1.3 81.8 - - + +
64A VAL* 1.3 83.2 + - + +
66A MET* 4.4 0.2 - - - -
67A ARG 3.2 15.8 + - - -
376A PRO* 3.6 15.6 - - + +
377A LEU* 3.6 31.8 - - + +
403A ASN* 3.2 19.3 + - - +
405A TYR* 3.4 43.8 - + + -
483A PRO* 5.5 0.2 - - - +
489A LEU* 3.8 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 3.6 31.9 - - + +
61A LEU* 2.9 19.3 + - + +
63A HIS* 1.3 97.4 - - + +
65A TYR* 1.3 67.0 + - - +
67A ARG* 3.1 12.2 + - + +
68A LYS* 3.2 25.9 + - + +
405A TYR* 4.1 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.7 20.8 - - - +
51A ASN* 4.3 0.6 + - - -
54A SER* 3.3 35.1 + - - -
55A LEU* 3.5 30.7 - - + +
58A SER* 3.7 28.7 - - - +
60A GLU* 4.0 6.6 - - - +
61A LEU 2.8 15.8 + - - +
62A PRO* 3.4 10.8 - - + +
64A VAL* 1.3 73.4 - - - +
66A MET* 1.3 69.6 + - + +
68A LYS* 3.4 7.8 + - + +
69A GLN* 3.2 53.1 + - + +
77A PHE* 5.6 0.2 - + - -
79A LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.9 3.4 - - + -
62A PRO* 2.9 26.5 + - - +
64A VAL 3.1 0.2 - - - -
65A TYR* 1.3 85.4 - - + +
67A ARG* 1.3 65.1 + - - +
69A GLN 3.5 0.2 + - - -
70A SER 3.2 15.8 + - - -
77A PHE* 3.3 29.1 - - + -
79A LEU* 4.5 9.2 - - + -
88A VAL* 2.8 39.7 - - + -
90A ASN* 3.4 4.6 - - - +
377A LEU* 3.5 35.7 - - + -
401A ILE* 3.6 19.5 - - + -
403A ASN* 3.6 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS 3.2 14.5 + - - +
64A VAL* 3.1 6.1 + - + +
66A MET* 1.3 77.4 - - - +
68A LYS* 1.3 66.1 + - + +
70A SER* 2.6 27.3 + - - +
71A GLN* 3.4 33.6 + - + +
90A ASN* 4.1 5.4 - - - -
403A ASN* 3.7 3.6 - - - +
405A TYR* 3.4 31.7 + - + -
406A SER* 4.1 17.1 + - - +
409A PHE* 2.9 41.8 + - - +
410A ASP* 5.0 0.6 - - - +
411A GLU* 4.2 20.6 + - - +
417A PRO* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 3.4 35.8 + - + +
64A VAL* 3.2 22.2 + - + +
65A TYR* 3.7 10.5 - - + +
67A ARG* 1.3 80.8 - - + +
69A GLN* 1.3 68.5 + - - +
71A GLN* 3.2 33.2 + - - +
72A VAL* 3.6 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.5 22.6 - - + +
65A TYR* 3.2 57.1 + - + +
66A MET 3.5 1.1 + - - +
67A ARG 3.3 0.2 - - - -
68A LYS* 1.3 82.5 - - - +
70A SER* 1.3 58.2 + - - +
72A VAL* 3.2 8.4 + - - +
73A TYR* 2.8 46.7 + - + +
77A PHE* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET 3.2 4.8 + - - -
67A ARG* 2.6 25.8 + - - +
69A GLN* 1.3 74.7 - - - +
71A GLN* 1.3 64.5 + - - +
74A GLY* 2.6 52.5 + - - -
75A GLU* 4.4 1.1 - - - -
77A PHE* 4.0 4.3 - - - -
90A ASN* 3.7 34.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 3.5 50.0 + - - +
68A LYS* 3.3 21.7 - - - +
70A SER* 1.3 84.6 + - - +
72A VAL* 1.3 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS 4.0 11.0 - - - +
69A GLN* 3.2 13.5 + - - +
70A SER 3.1 0.4 - - - -
71A GLN* 1.3 80.9 - - + +
73A TYR* 1.3 87.6 + - + +
74A GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 4.2 25.6 - - + +
42A GLY* 3.4 33.3 + - - -
43A PRO* 3.4 24.9 - - + +
44A PRO* 3.8 8.8 - - - +
69A GLN* 2.8 46.2 + - + +
72A VAL* 1.3 94.8 - - + +
74A GLY* 1.3 57.2 + - - +
76A ILE 4.4 4.9 - - - +
77A PHE* 3.8 19.5 - - + -
392A TYR* 5.0 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 2.6 40.1 + - - -
71A GLN 5.0 0.2 + - - -
72A VAL 3.7 1.2 - - - -
73A TYR* 1.3 74.4 - - - +
75A GLU* 1.3 66.0 + - - -
76A ILE* 3.2 5.3 + - - -
77A PHE* 3.7 7.3 - - - -
----------------------------------------------------------
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