Contacts of the helix formed by residues 19 - 29 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.4 20.4 - - - +
18D ILE* 1.3 79.8 - - - +
20D ALA* 1.3 59.2 + - - +
21D GLN* 3.1 13.9 + - - +
22D ILE* 2.8 32.2 + - - +
23D MET* 3.1 22.6 + - - +
167D LEU* 4.8 5.3 + - - +
168D GLN* 2.8 42.2 + - - +
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.3 27.2 - - + +
12D GLY* 3.9 12.1 - - - -
15D GLU* 3.0 17.6 + - - +
19D ASN* 1.3 71.0 - - - +
21D GLN* 1.3 65.8 + - - +
23D MET* 3.8 0.9 - - - +
24D GLN* 2.9 27.6 + - - +
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS* 2.8 32.3 + - - +
19D ASN* 3.1 13.5 + - - +
20D ALA* 1.3 81.4 - - - +
22D ILE* 1.3 62.5 + - - +
24D GLN* 3.9 3.9 - - - +
25D LEU* 3.0 34.3 + - + +
167D LEU* 3.8 28.2 - - + +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.9 13.0 - - + -
19D ASN* 2.8 22.7 + - - +
21D GLN* 1.3 77.4 - - - +
23D MET* 1.3 60.7 + - - +
25D LEU* 4.0 2.4 - - - +
26D HIS* 2.8 42.7 + - + +
163D HIS 3.9 16.4 - - - +
164D ALA* 3.7 19.3 - - - +
165D TYR* 4.1 16.8 - - - +
167D LEU* 4.0 22.2 - - + +
168D GLN* 3.6 43.7 - - + +
169D TYR* 5.4 0.9 - - + -
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.3 8.1 - - + -
9D TYR* 3.9 20.9 - - + +
10D ASP 5.6 0.7 - - - +
11D TYR* 3.5 32.1 - - + +
14D LEU* 3.7 29.2 - - + -
18D ILE* 3.5 31.0 - - + +
19D ASN 3.1 16.7 + - - +
20D ALA 3.2 1.0 + - - +
22D ILE* 1.3 77.9 - - - +
24D GLN* 1.3 62.5 + - - +
26D HIS* 3.8 5.4 - - - +
27D HIS* 3.0 29.8 + - - +
77D PHE* 6.0 1.3 - - - -
78D TRP* 4.1 26.5 - - + -
81D LEU* 5.0 1.8 - - + -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.6 43.0 - - + +
20D ALA* 2.9 18.1 + - - +
21D GLN* 3.9 4.5 - - - +
23D MET* 1.3 78.2 - - - +
25D LEU* 1.3 59.1 + - + +
28D SER* 2.8 45.2 + - - +
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.7 21.5 - - + +
170A LYS* 4.0 25.4 - - + -
171A ASN* 3.8 22.0 - - - +
21D GLN* 3.0 31.7 + - + +
22D ILE* 4.0 2.5 - - - +
24D GLN* 1.3 74.4 - - + +
26D HIS* 1.3 66.6 + - - +
28D SER* 4.4 0.2 - - - -
29D LYS* 2.9 36.8 + - + +
30D HIS* 3.1 11.6 + - + -
167D LEU* 3.6 27.4 - - + -
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Residues in contact with HIS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 2.8 32.3 + - + +
23D MET* 3.8 5.6 - - - +
25D LEU* 1.3 74.3 - - - +
27D HIS* 1.3 57.9 + - - +
30D HIS* 3.4 9.9 - - + +
31D HIS* 3.0 27.7 + - - +
74D HIS* 3.1 9.1 + + - -
77D PHE* 3.9 17.8 - + - -
78D TRP* 3.5 21.6 - + + -
159D ASP* 2.9 16.2 - - - -
163D HIS* 3.1 21.2 + + - +
164D ALA* 3.9 17.2 + - + +
199D MN 2.2 30.8 + - - -
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Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.6 31.3 - - + +
5D PRO 2.8 26.9 + - - -
6D ASP* 4.8 3.4 - - - -
7D LEU* 3.5 38.5 - - + +
11D TYR* 2.8 31.3 + + + -
23D MET 3.0 17.6 + - - +
26D HIS* 1.3 78.6 - - - +
28D SER* 1.3 60.9 + - - +
31D HIS* 3.6 3.7 - - - +
32D ALA 3.3 20.1 + - - -
78D TRP* 3.8 26.0 - - + -
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.6 4.9 - - - +
11D TYR* 3.7 15.9 - - - -
24D GLN* 2.8 34.8 + - - +
25D LEU* 4.4 0.2 - - - -
27D HIS* 1.3 77.6 - - - +
29D LYS* 1.3 81.4 + - - +
32D ALA* 3.1 18.2 - - - +
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.6 42.2 - - + +
25D LEU* 2.9 27.3 + - + +
28D SER* 1.3 98.4 + - - +
30D HIS* 1.3 59.8 + - - +
32D ALA* 3.8 1.2 - - - +
33D ALA* 3.0 30.5 + - - +
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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