Contacts of the helix formed by residues 9 - 27 (chain C) in PDB entry 4QPQ
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 SER 9 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ALA* 5.0 0.4 - - - -
40B SER* 4.8 0.2 + - - -
44B GLU* 3.4 17.2 + - - -
8C ILE* 1.3 83.1 - - - +
10C ASN* 1.3 64.3 + - - +
11C ASP* 3.7 10.4 + - - +
12C ALA* 3.1 23.6 + - - +
13C TYR* 3.0 19.1 + - - +
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Residues in contact with ASN 10 (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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2B ALA* 4.2 19.4 + - - +
9C SER* 1.3 73.0 - - - +
11C ASP* 1.3 66.9 + - - +
13C TYR* 3.6 7.9 - - + +
14C GLU* 3.0 40.0 + - + +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C SER* 3.2 9.6 - - - +
10C ASN* 1.3 77.3 - - - +
12C ALA* 1.3 60.0 + - - +
14C GLU* 3.3 12.1 + - - +
15C LYS* 3.0 47.7 + - - +
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 5.6 2.0 - - + -
44B GLU* 4.2 16.4 - - + +
47B LEU* 4.0 23.9 - - + +
8C ILE* 4.2 17.0 - - + -
9C SER* 3.1 20.7 + - - +
11C ASP* 1.3 79.4 - - - +
13C TYR* 1.3 62.1 + - - +
15C LYS* 3.4 4.0 + - - +
16C ILE* 3.0 30.7 + - + +
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Residues in contact with TYR 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA* 4.3 16.2 - - + -
3B LYS 5.5 1.8 - - - -
4B VAL* 4.1 17.0 - - + -
8C ILE* 3.8 10.3 - - + +
9C SER 3.0 16.8 + - - +
10C ASN* 3.6 9.2 - - - +
12C ALA* 1.3 77.3 - - - +
14C GLU* 1.3 70.5 + - + +
16C ILE* 3.4 6.1 + - - +
17C ASN* 3.2 44.0 + - - -
35C PHE* 3.6 32.4 - + - -
11Q C 5.5 2.9 + - - -
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Residues in contact with GLU 14 (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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10C ASN* 3.0 30.1 + - + +
11C ASP* 3.9 11.5 - - - +
13C TYR* 1.3 83.1 - - + +
15C LYS* 1.3 61.2 + - + +
17C ASN* 3.4 8.2 + - - +
18C ALA* 2.8 28.9 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.2 24.1 - - + +
48B ARG* 6.1 2.6 - - - +
51B GLU* 3.7 24.1 + - - +
11C ASP* 3.0 34.7 + - + +
12C ALA* 3.7 4.9 - - - +
14C GLU* 1.3 75.7 - - + +
16C ILE* 1.3 64.8 + - - +
18C ALA* 3.3 8.9 + - - +
19C ILE* 3.1 28.5 + - - +
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 31.2 - - + -
47B LEU* 4.6 3.4 - - + -
8C ILE* 4.3 7.2 - - + -
12C ALA 3.0 18.3 + - - +
13C TYR 3.7 4.7 - - - +
15C LYS* 1.3 73.8 - - - +
17C ASN* 1.3 63.7 + - - +
19C ILE* 3.1 19.8 + - + +
20C ILE* 3.1 14.1 + - + +
35C PHE* 3.6 37.9 - - + -
38C THR* 3.7 22.2 - - - +
39C ALA* 4.0 15.9 - - + +
42C LEU* 4.1 16.2 - - + -
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.2 48.2 + - - -
14C GLU* 3.7 9.9 - - - +
16C ILE* 1.3 77.4 - - - +
18C ALA* 1.3 62.2 + - - +
20C ILE* 3.3 11.9 + - - +
21C GLU* 3.0 39.3 + - + +
35C PHE* 3.4 22.5 - - - -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU 2.8 18.1 + - - +
15C LYS* 3.3 11.9 - - - +
16C ILE 3.2 0.2 - - - -
17C ASN* 1.3 76.6 - - - +
19C ILE* 1.3 61.9 + - + +
21C GLU* 3.6 10.8 + - - +
22C LYS* 3.2 38.4 + - - +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.2 10.3 - - + -
50B HIS* 3.7 37.9 - - + +
15C LYS 3.1 15.3 + - - +
16C ILE* 3.1 8.9 + - + +
18C ALA* 1.3 76.5 - - + +
20C ILE* 1.3 64.1 + - + +
22C LYS* 3.0 19.6 + - + +
23C ARG* 2.9 55.5 + - + +
38C THR* 5.2 9.6 - - - -
41C MET* 5.6 2.5 - - + -
42C LEU* 4.1 27.1 - - + -
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Residues in contact with ILE 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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16C ILE* 3.1 15.6 + - + +
17C ASN* 3.3 12.3 + - - +
19C ILE* 1.3 75.6 - - - +
21C GLU* 1.3 59.9 + - + +
23C ARG* 3.2 8.4 + - - +
24C ARG* 2.9 45.8 + - + +
33C VAL* 3.3 21.3 - - + +
34C SER 3.9 2.5 - - - +
35C PHE* 3.7 36.8 - - + +
38C THR* 3.6 30.3 - - + +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN* 3.0 29.6 + - + +
18C ALA* 3.9 9.4 - - - +
19C ILE 3.2 0.2 - - - -
20C ILE* 1.3 77.8 - - + +
22C LYS* 1.3 61.0 + - + +
24C ARG* 4.1 6.1 - - - +
25C GLN* 3.2 31.1 + - - +
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 6.4 0.2 - - - -
18C ALA* 3.2 27.5 + - - +
19C ILE* 3.0 18.9 + - + +
21C GLU* 1.3 77.3 - - + +
23C ARG* 1.3 60.4 + - + +
25C GLN* 3.1 8.1 + - - +
26C GLU* 2.8 45.4 + - - +
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Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 3.6 27.3 - - - -
19C ILE* 2.9 35.9 + - + +
20C ILE* 3.2 9.2 + - - +
22C LYS* 1.3 77.0 - - - +
24C ARG* 1.3 54.4 + - - +
26C GLU* 4.1 17.2 + - - -
27C GLY 2.7 31.5 + - - -
28C ALA* 3.2 9.9 - - + +
33C VAL* 3.9 27.6 - - + -
38C THR* 5.3 5.1 - - + +
41C MET* 3.9 21.8 - - - +
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Residues in contact with ARG 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 ILE* 2.9 30.1 + - + +
21C GLU* 4.1 6.1 - - - +
23C ARG* 1.3 75.6 - - - +
25C GLN* 1.3 57.5 + - - +
27C GLY 3.1 13.6 - - - +
28C ALA* 3.7 13.2 + - + +
30C GLU* 4.4 12.6 - - - +
31C LYS* 3.1 34.4 - - - +
33C VAL* 3.7 28.5 + - + +
34C SER* 5.8 1.4 - - - +
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Residues in contact with GLN 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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21C GLU* 3.2 22.3 + - - +
22C LYS* 3.1 9.3 + - - +
23C ARG 3.0 0.6 - - - -
24C ARG* 1.3 78.7 - - - +
26C GLU* 1.3 66.2 + - + +
27C GLY 3.6 2.6 - - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 2.8 27.3 + - + +
23C ARG* 3.9 22.4 + - - +
25C GLN* 1.3 76.6 - - + +
27C GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 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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23C ARG 2.7 12.7 + - - -
24C ARG 3.1 14.2 - - - +
25C GLN 3.6 3.5 - - - +
26C GLU* 1.3 81.1 - - - +
28C ALA* 1.3 63.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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