Contacts of the helix formed by residues 17 - 29 (chain Y) in PDB entry 6CP3
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 17 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12Y LEU* 3.5 24.1 - - - +
14Y GLY 5.2 0.2 - - - -
15Y VAL 3.1 10.8 + - - +
16Y GLU* 1.4 67.0 - - - +
18Y THR* 1.3 53.4 + - - +
19Y TYR 3.2 2.7 - - - -
20Y ALA* 3.0 14.0 + - - +
21Y THR* 2.7 34.8 + - - -
104Y ILE* 5.5 1.6 - - - -
107Y ASP* 4.5 17.3 - - - -
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Residues in contact with THR 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLU* 4.0 22.7 + - + +
11C SER* 3.6 20.5 + - - -
14C LEU* 4.5 3.5 - - - +
56F GLU* 5.0 2.7 + - - -
12Y LEU* 4.0 2.9 - - - +
13Y PHE* 5.8 1.6 - - - +
14Y GLY 4.7 12.4 + - - +
16Y GLU* 4.3 21.5 - - - +
17Y GLY* 1.3 78.1 - - - +
19Y TYR* 1.3 70.3 + - + +
21Y THR* 3.3 10.6 - - - -
22Y ALA* 2.8 30.3 + - - +
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Residues in contact with TYR 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 3.6 26.2 + - + +
14C LEU* 3.5 33.7 - - + -
18C ILE* 4.7 2.4 - - - +
16Y GLU* 4.2 5.3 + - - +
17Y GLY 3.2 0.6 - - - -
18Y THR* 1.3 85.6 - - + +
20Y ALA* 1.3 59.0 + - - +
22Y ALA* 3.4 5.3 + - - +
23Y LEU* 3.0 26.7 + - - +
88Y LEU* 5.0 11.9 - - + +
91Y VAL* 4.6 2.5 - - + -
92Y LEU* 2.3 55.4 - - + -
95Y ASN* 2.7 36.6 + - - +
97Y ARG* 4.0 7.4 - - + +
104Y ILE* 4.1 22.0 - - + -
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Residues in contact with ALA 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y GLY* 3.0 14.4 + - - +
19Y TYR* 1.3 78.1 - - - +
21Y THR* 1.3 54.2 + - - +
23Y LEU* 3.0 10.9 + - + +
24Y TYR* 2.6 38.2 + - - +
104Y ILE* 3.8 31.5 - - + +
107Y ASP* 4.8 4.9 - - + -
108Y PHE* 4.6 19.4 - - + +
111Y LEU* 5.6 3.4 - - + -
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Residues in contact with THR 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 5.0 8.1 - - - +
8Y PRO* 4.8 8.3 - - + -
11Y ARG* 4.0 27.2 + - - +
12Y LEU* 3.5 16.5 + - - +
13Y PHE 5.0 0.2 + - - -
17Y GLY 2.7 26.9 + - - -
18Y THR* 3.2 16.2 + - - -
20Y ALA* 1.3 72.5 - - - +
22Y ALA* 1.3 61.7 + - - +
24Y TYR* 3.2 7.1 + - + +
25Y GLN* 2.9 43.8 + - - +
111Y LEU* 5.2 7.4 - - + +
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Residues in contact with ALA 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 4.8 6.9 - - - +
14C LEU* 4.0 22.7 - - + -
15C GLU* 4.2 7.7 - - - +
18C ILE* 3.5 19.1 - - + -
18Y THR 2.8 19.2 + - - +
19Y TYR* 3.6 4.7 - - - +
21Y THR* 1.3 73.1 - - - +
23Y LEU* 1.3 58.8 + - - +
25Y GLN* 3.2 15.0 - - - +
26Y ALA* 2.8 33.1 + - - +
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Residues in contact with LEU 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 3.5 14.3 - - + +
19Y TYR 3.0 15.4 + - - +
20Y ALA* 3.2 12.1 - - + +
22Y ALA* 1.3 76.1 - - - +
24Y TYR* 1.3 64.1 + - - +
26Y ALA* 3.7 1.7 - - - +
27Y ALA* 3.0 26.9 + - + +
36Y ALA* 5.9 2.7 - - + -
40Y LEU* 4.5 12.1 - - + -
84Y TYR* 4.4 21.1 - - + +
85Y VAL* 4.3 27.8 - - + -
88Y LEU* 4.6 24.7 - - + -
104Y ILE* 5.7 4.7 - - + -
108Y PHE* 4.3 24.9 - - + -
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Residues in contact with TYR 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y PRO* 4.1 14.6 - - + -
9Y PRO* 3.4 36.8 - - + +
20Y ALA 2.6 20.2 + - - +
21Y THR* 3.2 5.4 + - - +
23Y LEU* 1.3 71.3 - - - +
25Y GLN* 1.3 56.2 + - - +
27Y ALA* 3.1 5.4 + - - +
28Y ALA* 2.6 52.9 + - + +
33Y ILE* 4.8 14.0 - - + +
108Y PHE* 3.9 25.5 - + + -
111Y LEU* 3.4 42.4 - - + -
112Y ASN* 5.6 2.0 - - - -
115Y HIS* 4.0 26.7 + + + -
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Residues in contact with GLN 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 3.4 36.0 + - - -
15C GLU* 4.0 18.0 + - + +
8Y PRO* 4.5 14.9 - - + +
21Y THR* 2.9 33.8 + - - +
22Y ALA* 3.2 18.5 - - - +
24Y TYR* 1.3 84.4 - - + +
26Y ALA* 1.3 60.5 + - - +
28Y ALA* 3.5 12.5 + - - +
29Y LYS* 3.2 24.4 + - - +
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Residues in contact with ALA 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 4.4 10.5 - - + +
18C ILE* 3.5 34.1 - - + -
19C LYS* 3.2 28.8 + - - +
22Y ALA 2.8 22.3 + - - +
23Y LEU 3.7 2.7 - - - +
25Y GLN* 1.3 73.5 - - - +
27Y ALA* 1.3 59.7 + - - +
29Y LYS* 3.4 16.0 - - - +
30Y ASN* 4.2 3.5 + - - +
84Y TYR* 3.3 8.2 + - + -
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Residues in contact with ALA 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y LEU* 3.0 21.4 + - + +
24Y TYR* 3.8 3.1 - - - +
26Y ALA* 1.3 76.7 - - - +
28Y ALA* 1.3 62.5 + - - +
29Y LYS 3.3 2.0 - - - -
30Y ASN* 3.3 6.6 + - - +
31Y SER 3.2 26.0 + - - +
32Y SER* 4.0 17.2 + - - +
33Y ILE* 4.2 8.5 - - + -
36Y ALA* 5.2 6.7 - - + -
84Y TYR* 3.9 20.6 - - + -
108Y PHE* 6.0 1.8 - - + -
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Residues in contact with ALA 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Y TYR* 2.6 41.1 + - + +
25Y GLN* 3.8 13.0 - - - +
26Y ALA 3.4 0.4 - - - -
27Y ALA* 1.3 75.1 - - - +
29Y LYS* 1.3 60.6 + - - +
30Y ASN 3.5 0.2 + - - -
31Y SER* 3.6 9.2 + - - -
33Y ILE* 4.4 8.3 - - + -
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Residues in contact with LYS 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 2.9 31.8 + - - -
19C LYS* 3.4 33.8 - - - +
25Y GLN 3.2 16.8 + - - +
26Y ALA* 3.4 14.6 - - - +
28Y ALA* 1.3 77.7 - - - +
30Y ASN* 1.3 57.4 + - + +
31Y SER 3.4 1.7 + - - -
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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