Contacts of the helix formed by residues 18 - 37 (chain C) in PDB entry 6QPA
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 LYS 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.2 19.1 + - + -
17C ASN* 1.3 78.6 + - - +
19C PRO* 1.3 78.3 - - + +
20C ASP* 3.1 31.5 + - + +
21C SER* 2.9 28.8 + - - +
22C TYR* 3.4 15.3 - - - -
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Residues in contact with PRO 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 1.3 88.7 - - + +
20C ASP* 1.3 66.6 + - - +
21C SER 3.2 0.3 + - - -
22C TYR* 3.3 13.7 + - + +
23C GLU* 3.2 19.8 + - - +
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Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.0 33.9 + - + -
19C PRO* 1.3 80.8 - - - +
21C SER* 1.3 61.9 + - - +
23C GLU* 3.2 9.0 + - - +
24C THR* 3.1 31.1 + - + +
109C MET* 5.9 0.4 - - - -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.5 7.9 - - - -
16C ALA* 2.7 35.1 + - - +
18C LYS* 2.9 11.6 + - - +
20C ASP* 1.3 75.7 - - - +
22C TYR* 1.3 63.4 + - - +
24C THR* 3.4 4.3 + - - -
25C MET* 2.9 33.2 + - - +
74C MET* 6.4 0.2 - - - -
109C MET* 3.4 37.6 - - - +
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASN* 3.0 28.4 + - - -
18C LYS 3.4 23.1 - - - -
19C PRO* 3.3 10.2 + - + +
21C SER* 1.3 77.2 - - - +
23C GLU* 1.3 62.8 + - - +
25C MET* 3.3 21.7 + - + +
26C MET* 3.2 25.8 + - - +
49C LEU* 3.6 24.6 - - + +
68C ARG* 4.8 3.6 + - - +
74C MET* 3.4 21.0 - - - +
302C MET* 6.3 2.7 - - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO 3.2 12.0 + - - +
20C ASP* 3.2 14.4 - - - +
21C SER 3.1 0.4 - - - -
22C TYR* 1.3 76.3 - - - +
24C THR* 1.3 67.0 + - + +
26C MET* 3.2 26.7 - - - +
27C LYS* 3.2 31.4 + - + +
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 3.1 17.8 + - + +
21C SER* 3.4 1.0 + - - -
23C GLU* 1.3 80.2 - - + +
25C MET* 1.3 59.9 + - - +
27C LYS* 4.4 6.5 - - - +
28C VAL* 2.8 44.6 + - - +
105C GLY 5.3 9.4 - - - +
106C CYS* 5.0 4.3 - - - -
109C MET* 3.2 32.7 - - + +
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Residues in contact with MET 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.0 22.4 - - + -
21C SER* 2.9 13.8 + - - +
22C TYR* 3.7 44.2 - - + +
23C GLU 3.2 0.2 - - - -
24C THR* 1.3 78.6 + - - +
26C MET* 1.3 57.3 + - - +
29C GLY* 3.2 26.9 + - - +
30C PRO* 3.6 2.3 - - - +
47C GLN* 4.4 21.1 + - - +
49C LEU* 4.3 13.9 - - + -
76C MET* 4.1 24.7 - - + +
106C CYS* 6.2 0.4 - - - -
109C MET* 4.0 19.1 - - + -
302C MET* 5.8 4.7 - - + -
303C MET* 4.9 2.3 - - - +
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Residues in contact with MET 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR 3.2 14.1 + - - +
23C GLU* 3.2 31.2 - - - +
25C MET* 1.3 77.1 - - - +
27C LYS* 1.3 60.4 + - + +
30C PRO* 3.2 23.5 - - - +
303C MET* 6.3 0.9 - - - -
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY* 6.3 3.1 - - - -
224A LEU* 3.5 27.5 - - - +
23C GLU* 3.2 26.4 + - + +
24C THR* 4.2 5.6 - - - +
26C MET* 1.3 83.4 - - + +
28C VAL* 1.3 69.0 + - + +
30C PRO* 4.1 2.9 - - - +
31C LYS* 3.3 31.1 + - - +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 4.9 15.5 - - + -
24C THR* 2.8 29.2 + - - +
27C LYS* 1.3 86.7 - - + +
29C GLY* 1.3 66.9 + - - +
30C PRO 3.4 0.7 - - - -
31C LYS* 3.0 17.7 + - - +
32C VAL* 3.2 13.7 + - + +
102C LEU* 3.5 41.7 - - + +
105C GLY* 5.4 3.8 - - - -
106C CYS* 3.5 23.3 - - - +
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C THR 3.7 1.2 + - - -
25C MET* 3.2 15.4 + - - +
28C VAL* 1.3 77.8 - - - +
30C PRO* 1.3 67.3 - - - +
32C VAL* 3.1 17.9 + - - +
33C CSS 3.2 16.5 + - - -
47C GLN* 4.7 6.7 - - - -
106C CYS* 5.5 1.0 - - - -
303C MET* 4.3 11.7 - - - -
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Residues in contact with PRO 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C MET 3.6 5.8 - - - +
26C MET* 3.2 28.0 - - - +
27C LYS 4.1 3.4 - - - +
28C VAL 3.6 2.9 - - - -
29C GLY* 1.3 88.5 - - - +
31C LYS* 1.3 57.8 + - + +
33C CSS 3.3 7.8 + - + +
34C ILE* 2.9 40.2 + - + +
303C MET* 4.2 19.7 - - + -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL* 3.1 34.3 - - + +
222A SER* 4.3 1.4 - - - -
223A THR 3.4 24.9 - - - +
224A LEU* 3.9 14.5 - - + +
27C LYS* 3.3 29.7 + - - +
28C VAL* 3.0 8.7 + - - +
30C PRO* 1.3 78.6 - - + +
32C VAL* 1.3 60.4 - - - +
34C ILE* 3.4 6.9 + - + +
35C THR* 2.9 28.4 + - - -
102C LEU* 3.7 27.4 - - + -
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.2 15.2 + - + +
29C GLY* 3.1 9.7 + - - +
31C LYS* 1.3 72.7 - - - +
33C CSS 1.3 65.2 + - - +
35C THR* 3.3 5.8 + - - -
36C THR* 2.7 42.8 + - - +
78C GLN* 6.6 0.2 - - + -
99C ILE* 5.4 12.3 - - + +
102C LEU* 4.0 27.6 - - + -
103C CSS 4.1 28.5 - - - -
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Residues in contact with CSS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY 3.2 13.7 + - - +
30C PRO* 3.3 8.9 + - + +
32C VAL* 1.3 84.5 + - - +
34C ILE* 1.3 64.1 + - + +
36C THR* 3.2 12.1 + - - -
37C ALA* 3.0 24.9 + - - +
42C PHE* 4.9 3.7 - - + -
45C PHE* 3.8 49.4 - - + -
78C GLN* 3.5 28.7 - - - -
80C THR* 4.1 15.7 - - - -
303C MET* 4.7 6.1 - - + -
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A MET* 4.0 24.7 - - + +
221A VAL* 3.8 29.6 - - + +
222A SER* 3.4 18.8 - - - +
30C PRO* 2.9 31.0 + - + +
31C LYS* 3.7 6.5 - - + +
32C VAL 3.2 0.4 - - - -
33C CSS 1.3 76.8 + - + -
35C THR* 1.3 62.1 + - - +
37C ALA* 3.4 14.9 + - - +
38C SER* 3.6 8.7 + - - -
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Residues in contact with THR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS* 5.7 1.6 - - - +
222A SER* 3.3 27.1 + - - -
31C LYS 2.9 14.6 + - - -
32C VAL* 3.5 9.6 - - - -
34C ILE* 1.3 77.2 - - - +
36C THR* 1.3 58.3 + - - +
38C SER* 2.7 30.0 + - - -
91C MET* 4.3 0.6 - - - +
95C ASN* 3.4 39.6 - - + +
98C GLU* 4.3 8.3 - - + -
99C ILE* 3.9 17.9 - - + -
102C LEU* 3.9 4.7 - - - +
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Residues in contact with THR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 2.7 27.8 + - - +
33C CSS 3.5 14.2 - - - -
35C THR* 1.3 78.7 - - - +
37C ALA* 1.3 57.0 - - - +
38C SER 3.0 5.4 + - - -
39C HIS* 3.2 13.9 + - - +
42C PHE* 3.5 26.0 - - + +
80C THR* 4.6 9.1 - - + +
82C TRP* 3.4 31.6 - - + -
91C MET* 3.7 26.5 - - + +
99C ILE* 5.5 1.4 - - - +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C CSS 3.0 15.9 + - - +
34C ILE* 3.9 7.9 - - - +
35C THR 3.3 0.8 - - - -
36C THR* 1.3 72.5 - - - +
38C SER* 1.3 61.9 + - - +
39C HIS 3.1 5.8 + - - +
42C PHE* 3.5 28.0 - - + -
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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
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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