Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 2P4K
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 ASN 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C GLU* 3.5 20.4 - - - +
18C ILE* 1.3 78.4 - - - +
20C ALA* 1.3 65.0 + - - +
21C GLN* 3.1 12.0 + - - +
22C ILE* 2.9 31.7 + - - +
23C MET* 3.2 18.5 + - - +
167C LEU* 4.6 6.1 + - - +
168C GLN* 2.9 42.2 + - - +
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Residues in contact with ALA 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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11C TYR* 3.4 19.1 - - + +
12C GLY* 3.8 18.2 - - - +
15C GLU* 3.0 18.7 + - - +
18C ILE 3.9 0.2 + - - -
19C ASN* 1.3 73.6 - - - +
21C GLN* 1.3 64.2 + - - +
23C MET* 3.2 2.1 + - - +
24C GLN* 2.9 24.5 + - - +
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Residues in contact with GLN 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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170B LYS* 2.9 37.2 + - - +
19C ASN* 3.1 11.7 + - - +
20C ALA* 1.3 77.8 - - - +
22C ILE* 1.3 59.5 + - - +
24C GLN* 3.4 6.3 + - + +
25C LEU* 2.9 40.5 + - + +
167C LEU* 3.8 25.5 - - + +
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Residues in contact with ILE 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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18C ILE* 3.9 15.0 - - + -
19C ASN* 2.9 21.6 + - - +
21C GLN* 1.3 75.8 - - - +
23C MET* 1.4 66.7 + - - +
25C LEU* 3.8 2.1 - - - +
26C HIS* 2.8 35.2 + - + +
163C HIS 3.9 13.9 - - - +
164C ALA* 3.6 19.3 - - - +
165C TYR* 3.9 23.3 - - - -
167C LEU* 3.9 23.1 - - + +
168C GLN* 3.8 38.6 - - + +
169C TYR* 5.4 1.1 - - + -
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Residues in contact with MET 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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7C LEU* 4.0 17.0 - - + -
9C TYR* 4.0 13.9 - - + +
10C ASP 5.6 0.4 - - - +
11C TYR* 3.4 38.3 - - + +
14C LEU* 4.0 19.5 - - + -
18C ILE* 3.6 31.4 - - + +
19C ASN 3.2 11.6 + - - +
20C ALA 3.2 0.9 + - - +
22C ILE* 1.4 79.2 - - - +
24C GLN* 1.4 56.8 + - - +
26C HIS* 3.8 4.4 - - - +
27C HIS* 2.9 34.5 + - - +
77C PHE* 6.1 1.1 - - - -
78C TRP* 3.7 35.4 - - + -
81C LEU* 4.8 2.5 - - + -
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Residues in contact with GLN 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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11C TYR* 3.3 42.8 - - + -
20C ALA 2.9 16.1 + - - +
21C GLN* 3.8 6.6 - - + +
23C MET* 1.4 75.7 - - - +
25C LEU* 1.3 59.4 + - + +
28C SER* 2.7 48.2 + - - +
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Residues in contact with LEU 25 (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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166B TYR* 3.7 22.4 - - + +
170B LYS* 4.1 20.6 - - + -
171B ASN* 4.0 20.9 - - - +
21C GLN* 2.9 32.3 + - + +
22C ILE* 3.9 2.5 - - - +
24C GLN* 1.3 81.5 - - + +
26C HIS* 1.3 64.6 + - - +
29C LYS* 2.9 38.0 + - + +
30C HIS* 3.0 12.3 + - + -
167C LEU* 3.5 31.4 - - + -
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Residues in contact with HIS 26 (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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22C ILE* 2.8 25.4 + - + +
23C MET* 3.8 6.0 - - - +
25C LEU* 1.3 78.0 - - - +
27C HIS* 1.3 59.3 + - - +
30C HIS* 3.3 9.4 - - + +
31C HIS* 3.0 27.5 + - - +
74C HIS* 3.1 12.6 + + - -
77C PHE* 4.0 12.8 - + - -
78C TRP* 3.5 23.3 - + + -
159C ASP* 2.9 18.2 - - - -
163C HIS* 3.2 20.8 + + - +
164C ALA* 3.9 16.5 - - + -
199C MN 2.2 30.2 + - - -
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Residues in contact with HIS 27 (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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4C LEU* 3.8 29.3 - - + +
5C PRO 2.7 29.4 + - - -
6C ASP* 4.6 4.5 - - - -
7C LEU* 3.7 32.3 + - + -
11C TYR* 2.7 34.6 + + + -
23C MET 2.9 17.5 + - - +
26C HIS* 1.3 79.6 - - - +
28C SER* 1.3 62.4 + - - +
31C HIS* 3.5 3.6 - - - +
32C ALA* 3.3 21.0 + - - +
78C TRP* 3.8 24.2 - - + -
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Residues in contact with SER 28 (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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4C LEU* 4.8 4.9 - - - +
11C TYR* 3.8 15.5 - - - -
24C GLN* 2.7 35.5 + - - +
25C LEU* 5.6 0.2 - - - +
27C HIS* 1.3 76.7 - - - +
29C LYS* 1.3 78.8 + - - +
32C ALA* 3.1 18.6 - - - +
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Residues in contact with LYS 29 (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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171B ASN* 3.8 41.5 + - + +
25C LEU* 2.9 28.3 + - + +
28C SER* 1.3 97.3 + - - +
30C HIS* 1.3 63.7 + - - +
31C HIS 3.6 0.2 - - - -
32C ALA* 3.8 1.4 - - - +
33C ALA* 3.0 25.8 + - - +
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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