Contacts of the helix formed by residues 15 - 24 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLU* 3.8 8.5 + - + +
14C ILE* 1.3 66.9 - - - +
16C GLU* 1.3 57.0 + - - +
17C SER* 2.4 29.1 + - - -
18C LEU* 3.0 15.4 + - + +
19C TYR* 2.8 40.0 + - + +
105C TYR* 2.8 43.2 + - + +
476C LYS* 3.6 13.4 + - - -
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Residues in contact with GLU 16 (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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14C ILE* 2.8 22.0 + - + +
15C ASP* 1.3 71.9 + - - +
17C SER* 1.3 60.6 + - - +
20C SER* 2.7 39.2 + - - +
23C LEU* 4.5 18.2 - - + -
826C ASP* 3.1 26.8 - - - +
852C ARG* 5.8 2.1 - - - +
853C GLN* 3.2 45.2 + - - +
856C LYS* 4.7 6.7 + - - +
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Residues in contact with SER 17 (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 ASP* 2.4 24.3 + - - -
16C GLU* 1.3 85.5 - - - +
18C LEU* 1.3 56.7 + - - +
20C SER* 5.2 0.9 - - - -
476C LYS* 3.4 32.3 + - - +
477C SER* 3.7 20.5 + - - -
824C ASP 6.0 1.8 - - - -
826C ASP* 5.6 5.2 - - - -
856C LYS* 5.6 3.6 - - - +
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Residues in contact with LEU 18 (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 ASP* 3.0 20.5 + - - +
17C SER* 1.3 80.9 + - - +
19C TYR* 1.3 91.7 + - + +
20C SER 3.5 1.2 + - - -
102C LEU 6.1 1.1 - - - +
103C ASN* 4.0 11.9 - - + +
105C TYR* 3.6 25.4 - - + -
476C LYS* 4.5 13.7 - - + +
477C SER* 4.3 8.7 - - - +
479C LEU* 4.3 28.3 - - + -
480C ASN* 3.3 32.5 + - + +
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Residues in contact with TYR 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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13C GLU 5.8 0.2 - - - -
14C ILE* 4.8 3.8 - - + -
15C ASP* 2.8 41.8 + - + +
16C GLU* 4.8 0.9 - - - -
18C LEU* 1.3 96.7 - - + +
20C SER* 1.3 65.0 + - - +
21C ARG 3.4 2.0 - - - -
22C GLN* 2.9 9.9 + - + -
23C LEU* 2.7 29.9 + - + -
31C MET* 3.5 32.8 - - + -
35C GLN* 4.5 14.8 + - - -
57C LEU 3.8 13.7 - - - -
58C ALA 3.7 17.7 - - - -
59C GLY* 3.7 9.3 - - - -
103C ASN* 3.0 22.9 + - - -
105C TYR* 3.9 17.1 - + - +
480C ASN* 3.6 18.8 - - - -
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Residues in contact with SER 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 GLU* 2.7 27.3 + - - +
17C SER* 5.0 1.3 - - - -
18C LEU 3.5 1.5 - - - -
19C TYR* 1.3 72.6 - - - +
21C ARG* 1.3 88.9 + - - -
23C LEU* 3.1 15.1 + - - +
24C TYR* 3.2 31.8 + - - -
477C SER* 4.7 11.7 - - - -
824C ASP* 5.6 0.4 - - - -
853C GLN* 5.4 2.3 + - - -
856C LYS* 4.2 15.6 + - - -
862C ILE* 4.3 1.7 - - - +
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Residues in contact with ARG 21 (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 LEU 5.4 0.2 + - - -
19C TYR 3.0 2.2 + - - -
20C SER* 1.3 93.8 + - - +
22C GLN* 1.3 60.6 + - - +
24C TYR* 3.6 11.7 + - - +
25C VAL* 3.6 4.5 - - - +
475C GLU* 5.5 4.2 + - - -
477C SER* 3.8 19.9 + - - +
478C ASN* 5.6 3.0 - - - +
480C ASN* 5.4 2.4 + - + +
481C ARG* 3.3 36.8 - - - +
823C LYS* 4.1 12.3 - - - +
824C ASP* 2.8 40.8 + - - -
862C ILE* 3.4 39.4 - - - +
863C ILE 4.1 5.8 - - - +
864C PRO* 3.6 5.0 - - - +
865C ALA* 3.0 38.0 + - + +
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Residues in contact with GLN 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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19C TYR* 2.9 10.8 + - - +
21C ARG* 1.3 74.0 - - - +
23C LEU* 1.3 60.9 + - - +
24C TYR 3.1 2.0 - - - -
25C VAL* 2.8 23.1 + - - +
26C LEU* 3.1 31.9 + - + +
31C MET* 3.3 20.7 - - - +
34C MET* 4.1 0.2 - - - +
57C LEU* 4.4 0.3 - - - +
58C ALA* 2.6 47.8 + - - +
480C ASN* 3.0 38.3 + - - +
865C ALA 3.3 10.6 + - - +
866C ILE* 4.2 16.5 - - + +
867C ALA 5.3 0.7 + - - -
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Residues in contact with LEU 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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14C ILE* 4.2 34.1 - - + -
16C GLU* 4.5 17.9 - - + -
19C TYR* 2.7 20.1 + - + +
20C SER* 3.1 12.3 + - - +
22C GLN* 1.3 73.8 - - - +
24C TYR* 1.3 62.0 + - + +
26C LEU 2.3 22.5 - - - +
27C GLY* 3.8 23.5 - - - +
28C LYS* 4.1 12.1 + - + +
31C MET* 3.4 27.1 - - - -
853C GLN* 5.2 11.2 - - + +
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Residues in contact with TYR 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 SER* 3.2 39.2 + - - -
21C ARG* 4.0 7.0 - - - +
22C GLN 3.1 1.4 - - - -
23C LEU* 1.3 84.4 - - + +
25C VAL* 1.3 61.6 + - - +
26C LEU 4.1 0.2 - - - -
853C GLN* 2.8 49.3 + - + +
854C LYS* 5.2 0.7 - - - -
856C LYS* 4.0 10.6 - - - +
857C PHE* 3.6 55.2 + + + -
862C ILE* 4.0 20.6 - - + -
864C PRO* 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