Contacts of the helix formed by residues 15 - 26 (chain A) in PDB entry 3CMM
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 ASP 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 4.6 2.8 + - - -
14A ILE* 1.3 68.5 - - - +
16A GLU* 1.3 58.3 + - - +
17A SER* 2.7 27.8 + - - -
18A LEU* 3.8 12.0 - - + +
19A TYR* 2.9 36.8 + - + +
105A TYR* 3.7 37.9 + - + +
476A LYS* 3.5 19.1 + - - -
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Residues in contact with GLU 16 (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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14A ILE* 3.2 13.2 + - + +
15A ASP* 1.3 70.9 + - - +
17A SER* 1.3 59.4 + - - +
20A SER* 2.8 38.7 + - - +
23A LEU* 3.9 25.4 - - + +
853A GLN* 2.6 46.5 - - + +
856A LYS* 5.9 1.0 + - - -
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Residues in contact with SER 17 (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 ASP* 2.7 19.0 + - - -
16A GLU* 1.3 77.0 - - - +
18A LEU* 1.3 56.3 + - - +
20A SER* 4.8 1.8 - - - -
476A LYS* 3.5 26.3 + - - +
477A SER* 3.2 31.5 + - - -
826A ASP* 5.8 4.5 - - - -
856A LYS* 6.4 0.4 - - - +
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Residues in contact with LEU 18 (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 ASP* 3.2 18.1 + - + +
17A SER* 1.3 82.8 + - - +
19A TYR* 1.3 97.4 + - + +
20A SER* 3.4 3.4 + - - -
21A ARG 5.2 0.2 + - - -
57A LEU 6.0 0.4 - - - +
102A LEU 6.0 2.0 - - - +
103A ASN* 4.0 17.3 - - - +
105A TYR* 4.0 14.8 - - + -
476A LYS* 4.3 14.8 - - - +
477A SER* 4.1 8.3 - - - +
479A LEU* 4.3 18.8 - - + -
480A ASN* 3.3 43.5 - - + +
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Residues in contact with TYR 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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14A ILE* 4.3 10.1 - - + -
15A ASP* 2.9 33.0 + - + +
18A LEU* 1.3 98.3 - - + +
20A SER* 1.3 54.8 - - - +
21A ARG 3.5 1.8 - - - -
22A GLN* 3.0 11.3 + - + -
23A LEU* 2.6 37.1 + - + +
31A MET* 3.5 31.0 - - + -
35A GLN* 3.8 18.7 + - - -
57A LEU 3.6 14.6 - - - -
58A ALA 3.4 19.5 - - - -
59A GLY* 3.4 11.3 - - - -
103A ASN* 3.0 23.6 + - - -
105A TYR* 4.1 12.5 - + - +
480A ASN* 3.6 15.7 - - - +
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Residues in contact with SER 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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16A GLU* 2.8 25.3 + - - +
17A SER* 4.7 0.9 - - - -
18A LEU 3.4 1.3 - - - -
19A TYR* 1.3 78.6 - - - +
21A ARG* 1.3 86.2 + - - -
23A LEU* 3.1 18.2 + - - +
24A TYR* 3.4 24.7 + - - -
477A SER* 4.3 16.8 - - - -
856A LYS* 4.7 11.2 + - - +
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Residues in contact with ARG 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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18A LEU 5.2 0.2 + - - -
19A TYR 3.5 0.4 - - - -
20A SER* 1.3 100.1 + - - +
22A GLN* 1.3 63.3 + - - +
24A TYR* 3.3 15.7 + - - +
25A VAL* 3.6 6.1 + - - +
475A GLU* 5.5 2.2 + - - -
477A SER* 3.9 23.0 + - - +
478A ASN* 4.9 2.2 + - - -
480A ASN* 5.2 1.1 - - + +
481A ARG* 3.2 43.4 - - - +
823A LYS* 5.1 3.2 - - - +
824A ASP* 3.1 37.8 + - - -
862A ILE* 3.6 42.0 - - - +
863A ILE 4.1 7.6 - - - -
864A PRO* 3.8 5.1 - - - +
865A ALA 3.6 29.3 + - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.0 8.3 + - - +
21A ARG* 1.3 78.8 - - - +
23A LEU* 1.3 58.6 + - - +
25A VAL* 3.0 7.9 + - - +
26A LEU* 2.9 50.1 + - + +
31A MET* 3.4 24.1 - - + +
34A MET* 4.0 0.6 - - - +
58A ALA* 2.8 40.1 + - - +
480A ASN* 3.2 37.6 + - - +
865A ALA 3.5 10.7 + - - +
866A ILE* 3.9 18.4 - - + +
867A ALA 5.5 0.2 + - - -
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Residues in contact with LEU 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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14A ILE* 3.7 25.1 - - + -
16A GLU* 3.9 34.1 - - + +
19A TYR 2.6 16.2 + - - +
20A SER* 3.2 14.8 - - - +
22A GLN* 1.3 75.0 - - - +
24A TYR* 1.3 57.8 + - + +
26A LEU 2.4 20.9 - - - +
27A GLY* 3.6 23.3 - - - +
28A LYS* 3.9 19.6 + - + +
31A MET* 3.7 17.5 - - - -
853A GLN* 6.3 0.2 - - + -
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Residues in contact with TYR 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 SER* 3.6 28.1 + - - -
21A ARG* 3.3 14.8 + - - +
22A GLN 3.2 1.0 - - - -
23A LEU* 1.3 80.2 - - + +
25A VAL* 1.3 63.1 + - - +
26A LEU 4.0 0.2 - - - -
853A GLN* 2.7 41.0 + - + +
854A LYS* 4.8 3.1 - - + -
856A LYS* 3.9 14.6 - - - +
857A PHE* 3.5 45.7 + + + +
862A ILE* 4.0 20.6 - - + -
864A PRO* 4.0 21.1 - - + +
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Residues in contact with VAL 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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21A ARG 3.8 8.3 - - - +
22A GLN* 3.0 9.5 + - - +
24A TYR* 1.3 79.2 - - - +
26A LEU* 1.3 70.7 + - + +
178A GLY 5.2 4.0 - - - +
381A LYS* 4.2 5.7 - - - -
382A PHE* 3.7 17.8 - - + -
570A GLY* 3.5 31.0 - - - -
571A THR* 4.0 27.6 - - + +
864A PRO* 3.6 15.5 - - + -
865A ALA 3.9 14.4 - - - +
866A ILE* 4.5 11.0 - - + -
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Residues in contact with LEU 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 GLN* 2.9 38.2 + - + +
23A LEU 2.4 31.5 - - - +
24A TYR 4.0 0.9 - - - -
25A VAL* 1.3 78.8 - - + +
27A GLY* 1.3 63.3 + - - +
30A ALA* 4.5 8.5 - - + -
31A MET* 4.0 7.9 - - + -
34A MET* 3.6 29.6 - - + -
372A GLN* 4.3 12.3 - - - +
375A LEU* 4.5 5.4 - - + -
379A SER* 5.9 1.6 - - - +
381A LYS* 4.5 9.4 - - + +
382A PHE* 3.5 30.3 - - + -
866A ILE* 4.1 12.8 - - + -
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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