Contacts of the helix formed by residues 34 - 50 (chain G) in PDB entry 6C6S
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 GLY 34 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLU 3.2 1.0 + - - -
33G ARG* 1.3 79.8 - - - +
35G PHE* 1.3 62.0 + - - +
36G GLY 3.2 2.8 + - - -
37G HIS* 3.9 5.1 + - - -
38G THR* 3.1 21.5 + - - -
199G ASP* 3.3 7.5 + - - -
45H ARG* 3.8 14.9 + - - +
49H SER* 5.2 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PHE* 4.3 12.8 - + - -
31G LEU* 4.4 15.9 - - + -
32G GLU* 3.3 37.4 + - + +
33G ARG 4.7 2.0 - - - -
34G GLY* 1.3 75.8 - - - +
36G GLY* 1.3 58.6 + - - +
37G HIS 3.5 0.2 - - - -
38G THR* 3.8 8.7 - - + -
39G LEU* 2.9 39.4 + - + +
46H ILE* 3.7 35.2 - - + -
50H SER* 3.2 31.2 - - - -
223H ILE* 3.6 25.6 - - + -
224H LEU* 5.4 1.3 - - + -
227H GLN* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.8 20.3 - - - +
32G GLU 4.1 1.6 + - - -
34G GLY 3.2 1.8 - - - -
35G PHE* 1.3 77.0 - - - +
37G HIS* 1.3 57.4 + - - +
39G LEU 3.9 0.3 - - - -
40G GLY 2.9 23.6 + - - -
187G VAL* 3.9 17.0 - - - -
199G ASP* 3.9 17.8 + - - -
201G LEU* 3.5 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY* 3.9 4.8 + - - -
36G GLY* 1.3 75.3 - - - +
38G THR* 1.3 56.9 + - - +
41G ASN* 2.9 32.2 + - - +
185G TYR* 4.1 14.2 + - + -
187G VAL* 3.5 35.5 - - + +
199G ASP* 5.8 3.4 - - - -
45H ARG* 3.4 31.5 - - - +
1213I TYR* 6.4 1.8 - + - -
1218I GLY* 5.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY 3.1 11.8 + - - -
35G PHE* 3.7 12.5 - - + -
36G GLY 3.2 0.6 - - - -
37G HIS* 1.3 78.2 - - - +
39G LEU* 1.3 64.2 + - + +
41G ASN* 4.0 2.9 - - - +
42G ALA* 3.0 25.1 + - + +
42H ALA* 3.8 39.7 - - + +
45H ARG* 3.0 34.7 + - + +
46H ILE* 4.3 15.6 - - + +
224H LEU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PRO* 4.7 3.6 - - + -
28G LEU* 5.2 6.5 - - + -
31G LEU* 3.9 28.9 - - + -
35G PHE* 2.9 22.6 + - + +
36G GLY 4.3 0.9 - - - +
38G THR* 1.3 78.4 - - + +
40G GLY* 1.3 58.3 + - - +
42G ALA* 4.3 7.0 - - + -
43G LEU* 2.8 41.2 + - + +
201G LEU* 4.2 11.0 - - + -
224G LEU* 5.3 2.7 - - + -
224H LEU* 3.8 29.4 - - + -
227H GLN* 4.3 22.7 - - + +
228H LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLY 2.9 19.2 + - - -
39G LEU* 1.3 76.7 - - - +
41G ASN* 1.3 57.2 + - - +
43G LEU* 3.9 2.2 - - - +
44G ARG 2.9 23.9 + - - -
185G TYR* 3.2 36.4 - - - +
201G LEU* 3.8 12.5 - - - +
203G ILE* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G HIS 2.9 15.4 + - - +
38G THR* 4.0 3.4 - - - +
40G GLY* 1.3 73.1 - - - +
42G ALA* 1.3 65.0 + - - +
44G ARG* 3.4 7.3 + - - +
45G ARG* 3.0 24.1 + - - +
185G TYR* 3.3 18.7 + - - +
38H THR* 5.0 2.7 - - - +
41H ASN* 3.0 17.0 - - - +
45H ARG* 6.3 1.1 - - - -
1087I TYR* 4.6 3.5 + - - -
1215I GLY* 3.5 15.0 - - - +
1216I ARG 2.9 28.1 + - - -
1217I THR 5.0 0.4 - - - +
1218I GLY* 3.2 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G THR 3.0 19.0 + - - +
39G LEU* 3.8 8.3 - - + +
41G ASN* 1.3 78.4 - - - +
43G LEU* 1.3 58.5 + - - +
45G ARG* 3.3 3.5 + - - +
46G ILE* 2.9 34.1 + - - +
224G LEU* 3.9 21.8 - - + -
38H THR* 3.5 20.6 - - - +
42H ALA* 5.0 12.1 - - + -
224H LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 4.1 22.4 - - + -
39G LEU* 2.8 34.0 + - + +
40G GLY 4.2 2.0 - - - +
42G ALA* 1.3 73.7 - - - +
44G ARG* 1.3 61.1 + - - +
46G ILE* 4.3 1.1 - - - +
47G LEU* 2.9 36.4 + - - +
201G LEU* 4.6 0.4 - - + -
203G ILE* 4.3 10.8 - - + -
217G ILE* 3.7 30.5 - - + -
220G ALA* 3.7 28.0 - - + -
221G ALA* 4.2 13.9 - - + +
224G LEU* 4.4 15.0 - - + -
228H LEU* 5.4 2.5 - - + -
231H PHE* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLY 2.9 19.3 + - - +
41G ASN* 3.7 8.0 + - - +
43G LEU* 1.3 76.8 - - - +
45G ARG* 1.3 63.3 + - - +
47G LEU* 4.0 0.5 - - - +
48G LEU* 3.0 50.3 + - + +
183G ILE* 3.5 42.5 + - + +
185G TYR* 3.8 24.7 - - + -
203G ILE* 5.7 0.6 - - - +
1082I ILE 5.0 1.8 + - - -
1083I GLU* 3.4 27.7 + - - +
1085I MET 5.2 0.6 + - - -
1087I TYR* 3.4 50.7 - - - +
1091I GLY 3.9 10.3 + - - -
1093I PRO* 4.0 13.1 - - - +
1215I GLY* 4.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ASN* 3.0 16.5 + - - +
42G ALA 3.4 9.6 - - - +
44G ARG* 1.3 79.4 - - - +
46G ILE* 1.3 60.6 + - + +
48G LEU 3.9 0.3 - - - -
49G SER* 2.9 34.7 + - - +
34H GLY* 3.0 27.8 + - - +
35H PHE* 5.3 0.7 - - + -
37H HIS* 3.5 21.0 - - - +
38H THR* 3.7 29.2 - - + +
1083I GLU* 3.4 33.9 + - - +
1084I ASP* 3.2 21.3 + - - -
1215I GLY 2.4 37.8 + - - -
1216I ARG* 3.4 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ALA 2.9 18.5 + - - +
43G LEU* 4.2 1.3 - - - +
44G ARG 3.3 0.2 - - - -
45G ARG* 1.3 75.5 - - - +
47G LEU* 1.3 65.8 + - - +
49G SER* 3.1 15.2 + - - +
50G SER 3.1 14.9 + - - +
51G MET* 4.3 0.5 - - - +
220G ALA* 3.7 32.5 - - + +
223G ILE* 3.7 30.1 - - + -
224G LEU* 4.0 29.6 - - + -
35H PHE* 3.5 33.0 - - + -
38H THR* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU 2.9 21.7 + - - +
44G ARG 4.0 2.2 - - - +
46G ILE* 1.3 77.2 - - - +
48G LEU* 1.3 61.5 + - - +
50G SER 4.5 0.2 + - - -
51G MET* 3.3 26.1 - - + +
180G VAL* 3.2 20.6 - - + +
183G ILE* 4.1 32.5 - - + -
203G ILE* 4.5 3.1 - - + -
205G MET* 3.7 27.1 - - + -
216G ALA* 3.4 43.7 - - + +
217G ILE* 4.1 11.4 - - + +
220G ALA* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ARG* 3.0 61.7 + - + +
47G LEU* 1.3 77.3 - - - +
49G SER* 1.3 64.6 + - - +
51G MET 5.4 0.2 + - - -
178G SER* 4.1 14.4 + - - -
180G VAL* 3.7 19.5 - - + -
181G GLU 4.7 5.6 - - - +
182G ARG* 4.6 11.2 - - - +
183G ILE* 3.7 18.2 - - + +
821I ARG* 4.9 9.4 - - - +
1082I ILE* 4.8 19.8 - - + +
1083I GLU* 3.7 25.0 - - + +
1093I PRO* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ARG* 2.9 24.1 + - - -
46G ILE* 3.1 11.3 + - - -
47G LEU 3.3 0.2 - - - -
48G LEU* 1.3 81.0 - - - +
50G SER* 1.3 80.3 + - - +
51G MET 4.0 2.1 + - - -
151G GLY* 4.4 16.3 + - - -
178G SER* 5.5 1.2 + - - -
33H ARG 5.3 6.7 - - - -
34H GLY* 6.1 0.7 - - - -
35H PHE* 3.8 16.4 - - - -
1083I GLU* 3.3 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE 3.1 4.9 + - - +
48G LEU 3.8 0.2 - - - -
49G SER* 1.3 91.4 + - - +
51G MET* 1.3 71.9 + - - +
52G PRO* 4.3 2.7 - - - +
150G ARG* 4.1 19.4 + - - +
223G ILE* 3.5 19.2 - - - +
8H PHE* 3.6 32.0 - - - -
32H GLU* 4.9 6.6 + - - +
35H PHE* 4.3 6.8 - - - -
----------------------------------------------------------
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