Contacts of the helix formed by residues 11 - 20 (chain C) in PDB entry 3L73
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 LEU 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C HIS* 3.1 18.4 - - + +
10C PRO* 1.3 81.0 - - + +
12C LEU* 1.3 62.3 + - + +
13C LYS 3.0 1.3 - - - -
14C MET* 2.7 39.3 + - - +
15C ILE* 3.1 17.0 + - + +
196P ILE* 4.1 32.1 - - + -
199P THR* 5.1 8.7 - - + -
200P PHE* 4.1 26.9 - - + -
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Residues in contact with LEU 12 (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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5C ILE* 3.5 35.2 - - + +
6C ARG* 3.7 12.5 - - + +
9C HIS* 3.0 28.1 - - + +
11C LEU* 1.3 75.5 - - + +
13C LYS* 1.3 53.9 + - - +
15C ILE* 2.8 25.4 + - + +
16C ASN* 2.6 35.9 + - - +
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Residues in contact with LYS 13 (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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6C ARG 3.3 13.5 + - - -
7C LYS* 3.2 25.8 - - - +
8C SER* 3.8 13.0 + - - +
9C HIS 2.8 21.3 + - - +
10C PRO* 4.4 10.4 - - + +
12C LEU* 1.3 78.5 - - - +
14C MET* 1.3 59.9 + - + +
16C ASN* 3.6 0.8 - - - +
17C ASN* 2.9 54.2 + - - +
203P GLU* 5.6 6.3 + - - -
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Residues in contact with MET 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 PRO 3.3 22.7 - - - +
11C LEU* 2.7 29.0 + - + +
13C LYS* 1.3 76.0 - - + +
15C ILE* 1.3 63.3 + - + +
17C ASN* 3.5 10.3 + - - +
18C SER* 2.8 23.2 + - - -
14P MET* 6.2 2.5 - - + -
199P THR* 5.1 14.6 - - + +
2010P BOG 3.7 26.5 - - - +
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Residues in contact with ILE 15 (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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11C LEU* 3.1 11.6 + - + +
12C LEU* 2.8 31.1 + - + +
14C MET* 1.3 76.4 - - + +
16C ASN* 1.3 61.9 + - - +
18C SER* 3.4 4.4 + - - -
19C LEU* 3.1 39.5 + - + +
20C ILE* 4.0 15.2 + - + -
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Residues in contact with ASN 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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6C ARG* 2.8 43.5 + - + +
7C LYS* 4.2 13.5 - - - +
12C LEU 2.6 19.5 + - - +
13C LYS* 3.6 1.8 - - - +
15C ILE* 1.3 69.9 - - - +
17C ASN* 1.3 78.4 + - - +
18C SER 2.9 10.6 + - - -
20C ILE* 3.2 15.7 + - - +
21C ASP* 2.8 67.0 + - - +
22C LEU 3.8 0.2 + - - -
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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
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13C LYS* 2.9 42.9 + - - +
14C MET* 3.5 5.2 + - - +
15C ILE 3.5 0.4 - - - -
16C ASN* 1.3 91.3 + - - +
18C SER* 1.3 60.6 + - - +
21C ASP* 5.1 3.1 - - - +
22C LEU* 3.9 22.9 - - - +
202C HIS* 4.4 5.4 + - - -
2G ILE 5.2 11.6 + - - +
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Residues in contact with SER 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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14C MET 2.8 20.3 + - - -
15C ILE* 3.6 5.2 + - - -
16C ASN 2.9 0.4 + - - -
17C ASN* 1.3 78.3 - - - +
19C LEU* 1.3 79.0 + - - +
22C LEU* 3.8 14.8 - - - +
202C HIS* 3.3 27.6 - - - -
2002C UQ 3.6 15.7 - - - +
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Residues in contact with LEU 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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15C ILE* 3.1 25.7 + - + +
18C SER* 1.3 94.3 - - - +
20C ILE* 1.3 68.9 + - + +
22C LEU* 4.2 0.4 - - - +
221C PHE* 3.0 51.8 - - + -
222C HIS* 3.9 4.9 - - - +
226C SER* 5.4 0.5 - - - -
2002C UQ 4.2 36.6 - - + -
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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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436A ARG* 3.1 35.4 + - - +
2008A PEE 5.8 8.7 - - + -
6C ARG* 4.3 15.9 - - + +
15C ILE* 4.4 14.8 - - + +
16C ASN* 3.2 23.4 + - + +
19C LEU* 1.3 90.4 - - + +
21C ASP* 1.3 75.6 + - - +
22C LEU 3.3 5.5 + - - +
220C PRO* 3.7 3.3 - - - +
221C PHE* 3.8 0.8 + - - +
222C HIS* 3.5 32.0 + - + +
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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