Contacts of the helix formed by residues 18 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.3 21.5 + - + -
17A ASN* 1.3 78.5 + - - +
19A PRO* 1.3 80.7 - - + +
20A ASP* 3.5 33.7 + - - +
21A SER* 2.9 25.0 + - - +
22A TYR* 3.2 15.5 - - - -
108A GLY 5.4 7.0 + - - -
109A MET* 6.1 2.1 - - - +
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 1.3 87.9 - - + +
20A ASP* 1.3 66.7 + - - +
22A TYR* 3.1 14.0 + - + +
23A GLU* 2.9 22.7 + - - +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.1 34.7 + - - +
19A PRO* 1.3 81.8 - - - +
21A SER* 1.3 56.8 + - - +
23A GLU* 3.3 7.6 + - - +
24A THR* 3.0 38.0 + - + +
109A MET* 5.8 0.7 - - - -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.6 6.7 - - - -
16A ALA* 2.6 35.6 + - - +
18A LYS* 2.9 12.6 + - - +
20A ASP* 1.3 75.5 - - - +
22A TYR* 1.3 62.4 + - - +
24A THR* 3.3 3.3 + - - -
25A MET* 3.0 35.3 + - - +
74A MET* 6.3 0.2 - - - -
109A MET* 3.4 36.8 - - - +
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN* 3.0 31.1 + - - -
18A LYS 3.2 31.2 - - - -
19A PRO* 3.1 10.4 + - + +
21A SER* 1.3 78.5 - - - +
23A GLU* 1.3 64.2 + - - +
25A MET* 3.4 18.9 + - + +
26A MET* 3.4 23.4 + - - +
49A LEU* 3.6 22.3 - - + +
68A ARG* 4.6 4.5 + - - +
74A MET* 3.4 22.3 - - - +
302A MET* 6.1 4.5 - - + -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO 2.9 12.3 + - - +
20A ASP* 3.5 11.7 - - - +
21A SER 3.2 0.2 - - - -
22A TYR* 1.3 77.8 - - - +
24A THR* 1.3 64.8 + - + +
25A MET 3.3 0.3 + - - -
26A MET* 3.3 25.7 + - - +
27A LYS* 3.2 26.6 + - + +
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP* 3.0 19.8 + - + +
21A SER* 3.3 1.1 + - - -
23A GLU* 1.3 78.9 - - + +
25A MET* 1.3 59.1 + - - +
27A LYS* 4.4 8.1 - - + +
28A VAL* 2.8 43.4 + - - +
105A GLY 5.4 9.4 - - - +
106A CYS* 5.2 5.5 - - - -
109A MET* 3.2 32.1 - - + +
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.8 22.7 - - + -
21A SER* 3.0 16.1 + - - +
22A TYR* 3.6 47.1 - - + +
23A GLU 3.2 0.4 - - - -
24A THR* 1.3 78.5 + - - +
26A MET* 1.3 56.5 + - - +
29A GLY* 3.3 25.0 + - - +
30A PRO* 3.6 2.6 - - - +
47A GLN* 4.3 13.8 + - - +
49A LEU* 4.3 13.2 - - + -
74A MET* 6.0 0.2 - - - -
76A MET* 4.2 22.7 - - + +
106A CYS* 6.4 0.7 - - - -
109A MET* 3.7 19.7 - - + -
302A MET* 5.8 4.3 - - + -
303A MET* 3.9 8.6 - - + +
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR 3.4 10.8 + - - +
23A GLU* 3.4 32.1 - - - +
25A MET* 1.3 79.1 - - - +
27A LYS* 1.3 60.4 + - + +
30A PRO* 3.2 23.0 - - + +
303A MET* 4.5 9.6 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.2 23.2 + - + +
24A THR* 4.2 4.6 - - + +
26A MET* 1.3 80.1 - - + +
28A VAL* 1.3 74.8 + - + +
30A PRO* 4.3 2.5 - - - +
31A LYS* 3.5 33.3 + - - +
224B LEU* 3.7 33.2 - - + +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 2.8 25.6 + - - +
27A LYS* 1.3 100.6 - - + +
29A GLY* 1.3 66.3 + - - +
30A PRO 3.5 0.9 - - - -
31A LYS* 3.0 17.4 + - - +
32A VAL* 3.2 12.2 + - + +
102A LEU* 3.5 41.5 - - + +
105A GLY* 5.5 3.8 - - - -
106A CYS* 3.5 22.7 - - - +
224B LEU* 4.6 11.7 - - + -
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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