Contacts of the helix formed by residues 34 - 50 (chain H) in PDB entry 6C6U
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 3.0 42.1 + - - +
49G SER* 6.3 0.9 - - - -
32H GLU 3.1 0.2 + - - -
33H ARG* 1.3 75.2 - - - +
35H PHE* 1.3 68.5 + - - +
36H GLY 3.5 2.5 - - - -
37H HIS* 4.5 1.1 - - - -
38H THR 4.0 1.4 + - - -
199H ASP* 2.8 18.7 + - - -
1081I PRO* 5.7 4.0 - - - -
1083I GLU* 5.0 7.9 - - - -
1084I ASP* 5.8 0.4 - - - -
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Residues in contact with PHE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ARG* 5.0 1.8 - - + -
46G ILE* 3.6 21.1 - - + -
49G SER* 3.5 31.6 - - - -
50G SER* 4.6 9.6 - - - -
223G ILE* 4.2 18.2 - - + -
227G GLN* 3.8 34.3 - - + +
8H PHE* 4.5 8.3 - + - -
31H LEU* 3.6 14.5 - - + +
32H GLU* 2.9 39.0 + - + +
33H ARG 4.6 4.0 - - - -
34H GLY* 1.3 84.9 - - - +
36H GLY* 1.3 64.5 + - - +
37H HIS 3.3 2.2 - - - -
38H THR* 3.4 16.4 - - + +
39H LEU* 3.0 28.6 + - + +
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Residues in contact with GLY 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.8 15.6 - - - +
34H GLY 3.5 0.6 - - - -
35H PHE* 1.3 77.3 - - - +
37H HIS* 1.3 56.8 + - - +
39H LEU* 4.1 0.3 - - - -
40H GLY* 2.9 24.3 + - - -
187H VAL* 3.8 17.4 - - - +
199H ASP* 3.9 18.7 - - - +
201H LEU* 3.5 18.2 - - - +
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Residues in contact with HIS 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ARG* 3.4 32.3 - - - +
34H GLY* 4.2 0.8 + - - -
35H PHE 3.3 0.2 - - - -
36H GLY* 1.3 77.1 - - - +
38H THR* 1.3 57.6 + - - +
41H ASN* 2.9 32.6 + - - +
185H TYR* 3.7 26.5 + + + +
187H VAL* 4.2 23.1 + - + +
199H ASP* 4.5 11.9 - - - -
1084I ASP* 4.7 3.4 - - - -
1216I ARG* 3.5 60.0 + - + +
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Residues in contact with THR 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ALA* 3.8 30.7 + - - +
45G ARG* 3.7 24.3 - - + +
46G ILE* 4.5 11.4 - - + -
224G LEU* 4.8 4.9 - - + +
34H GLY 4.1 0.7 - - - +
35H PHE* 3.4 36.3 + - + +
37H HIS* 1.3 78.7 - - - +
39H LEU* 1.3 68.0 - - + +
41H ASN* 4.1 3.7 - - - +
42H ALA* 3.0 28.9 + - - +
1216I ARG 5.9 0.4 - - - -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G LEU* 5.0 8.1 - - + -
227G GLN* 4.0 35.7 - - + +
228G LEU* 3.7 29.8 - - + -
231G PHE* 5.2 12.6 - - + -
11H PRO* 5.8 2.0 - - + -
28H LEU* 5.4 3.4 - - + -
31H LEU* 3.7 23.1 - - + -
35H PHE* 3.0 17.8 + - + +
38H THR* 1.3 82.7 - - + +
40H GLY* 1.3 61.8 + - - +
42H ALA* 4.5 4.3 - - + -
43H LEU* 3.0 41.7 + - + +
201H LEU* 4.3 13.7 - - + -
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Residues in contact with GLY 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLY 2.9 18.5 + - - -
37H HIS 3.9 0.7 - - - -
39H LEU* 1.3 77.4 - - - +
41H ASN* 1.3 55.1 + - - +
43H LEU* 4.3 0.8 - - - +
44H ARG* 2.8 32.2 + - - +
185H TYR* 4.0 27.4 - - - -
201H LEU* 4.0 10.8 - - - +
203H ILE* 4.7 5.8 - - - +
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Residues in contact with ASN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ASN* 3.1 21.0 - - - +
37H HIS 2.9 20.1 + - - +
38H THR* 4.1 4.3 - - - +
40H GLY* 1.3 73.1 - - - +
42H ALA* 1.3 60.6 + - - +
44H ARG* 4.0 16.1 + - - -
45H ARG* 2.9 47.6 + - - +
185H TYR* 4.2 11.1 - - - +
1216I ARG 3.1 10.3 + - - +
1217I THR* 2.7 31.6 + - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G THR* 4.2 18.4 - - + -
42G ALA* 5.3 8.5 - - + -
224G LEU* 5.9 2.0 - - + -
38H THR* 3.0 20.7 + - - +
39H LEU* 4.0 7.0 - - + +
41H ASN* 1.3 77.4 - - - +
43H LEU* 1.3 63.7 + - + +
45H ARG* 3.4 0.9 + - - +
46H ILE* 3.0 32.3 + - - +
224H LEU* 3.8 25.4 - - + -
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 4.9 16.2 - - + -
231G PHE* 3.7 39.9 - - + -
28H LEU* 5.8 0.9 - - + -
39H LEU* 3.0 28.0 + - + +
40H GLY* 4.3 2.9 - - - +
42H ALA* 1.3 82.6 - - + +
44H ARG* 1.3 57.4 + - - +
46H ILE* 4.1 5.3 - - + +
47H LEU* 3.0 43.0 + - + +
201H LEU* 5.8 3.1 - - + -
203H ILE* 5.4 16.6 - - + -
217H ILE* 4.0 20.4 - - + -
220H ALA* 4.7 13.0 - - + -
221H ALA* 5.4 2.5 - - - -
224H LEU* 4.9 2.7 - - + -
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Residues in contact with ARG 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H GLY 2.8 21.2 + - - +
41H ASN* 3.8 18.7 + - - +
42H ALA 3.3 0.2 - - - -
43H LEU* 1.3 76.4 - - - +
45H ARG* 1.3 63.1 + - - +
48H LEU* 2.9 45.3 + - + +
183H ILE* 3.4 37.5 - - + +
184H ALA* 5.2 1.7 - - - +
185H TYR* 3.7 33.5 + - + -
1217I THR* 4.1 22.0 - - - +
1219I GLU* 4.2 15.0 + - - -
538J ARG* 4.4 40.2 + - - +
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Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY* 3.6 25.0 + - - +
37G HIS* 4.0 25.7 - - - +
38G THR* 3.2 34.0 + - - +
41H ASN* 2.9 39.2 + - - +
42H ALA 4.1 0.9 - - - +
44H ARG* 1.3 85.2 - - - +
46H ILE* 1.3 58.6 + - - +
48H LEU* 4.9 2.5 - - - -
49H SER* 3.0 47.0 + - - +
50H SER* 4.9 0.2 + - - -
1217I THR 4.9 5.0 + - - -
1219I GLU* 4.0 22.2 + - - +
538J ARG 5.1 5.9 + - - -
539J SER* 5.9 2.8 - - - +
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Residues in contact with ILE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G PHE* 4.4 16.4 - - + -
38G THR* 4.6 11.0 - - + +
42H ALA 3.0 20.0 + - - +
43H LEU* 4.1 5.4 - - + +
45H ARG* 1.3 78.2 - - - +
47H LEU* 1.3 64.2 + - - +
50H SER* 2.9 45.2 + - - +
51H MET* 3.9 1.5 - - - +
220H ALA* 4.1 27.6 - - + +
223H ILE* 4.3 15.0 - - + -
224H LEU* 3.6 47.6 - - + -
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.0 29.3 + - + +
46H ILE* 1.3 77.0 - - - +
48H LEU* 1.3 60.5 + - - +
49H SER 3.4 0.3 + - - -
50H SER 4.3 0.7 + - - -
51H MET* 3.4 30.3 - - + +
178H SER* 4.0 4.3 - - - -
180H VAL* 3.3 33.2 - - + +
183H ILE* 3.7 18.2 - - + -
203H ILE* 5.9 3.8 - - + -
205H MET* 4.1 22.7 - - - -
216H ALA* 3.6 27.8 - - + +
217H ILE* 5.0 9.0 - - + -
220H ALA* 3.7 16.6 - - + -
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Residues in contact with LEU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ARG* 2.9 27.4 + - + +
45H ARG* 4.6 2.0 - - + +
47H LEU* 1.3 77.8 - - - +
49H SER* 1.3 64.5 + - - +
151H GLY 5.9 0.7 - - - -
152H TYR* 5.5 6.8 - - - +
178H SER* 4.7 6.4 + - - -
180H VAL* 4.2 8.3 - - + -
181H GLU 5.7 1.6 - - - +
183H ILE* 3.7 28.3 - - + +
535J ARG* 3.9 35.1 - - + +
538J ARG* 4.1 23.1 - - + +
539J SER* 3.6 36.7 - - - +
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Residues in contact with SER 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ARG 5.9 0.7 - - - -
34G GLY* 5.5 11.9 - - - -
45H ARG* 3.0 34.6 + - - +
47H LEU 4.6 0.4 - - - -
48H LEU* 1.3 90.2 - - - +
50H SER* 1.3 61.8 + - - +
51H MET 4.1 0.9 - - - -
150H ARG 3.9 1.0 - - - +
151H GLY* 3.3 22.7 - - - -
152H TYR 4.4 1.2 + - - -
178H SER* 5.8 1.1 - - - -
539J SER* 4.5 10.3 - - - -
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Residues in contact with SER 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PHE* 4.7 12.7 - - - -
33G ARG 5.0 9.0 - - - -
34G GLY* 6.4 0.7 - - - -
35G PHE* 3.8 29.4 - - - -
46H ILE* 2.9 29.7 + - - +
47H LEU 4.3 0.2 + - - -
49H SER* 1.3 80.9 - - - +
51H MET* 1.3 61.2 - - - +
150H ARG* 3.9 13.2 - - - -
223H ILE* 4.4 7.1 - - - +
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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) + - + + + + + -
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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