Contacts of the helix formed by residues 20 - 30 (chain D) in PDB entry 1Y67
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 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLU* 3.6 16.4 - - - +
19D ILE* 1.3 75.6 - - - +
21D ALA* 1.3 65.6 + - - +
22D ARG* 3.9 8.3 - - + +
23D THR* 2.7 46.5 + - - +
24D MET* 3.0 21.4 + - - +
178D ALA 5.6 0.3 - - - +
179D TYR* 5.9 0.5 - - - -
181D LEU* 3.8 10.7 - - - +
182D ASN* 3.2 39.2 - - - +
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Residues in contact with ALA 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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12D TYR* 3.3 28.6 - - + +
13D ASP* 3.8 19.5 - - + -
16D GLU* 3.1 19.2 + - - +
19D ILE 3.8 0.6 + - - -
20D ASP* 1.3 69.3 - - - +
22D ARG* 1.3 65.2 + - - +
24D MET* 3.4 2.1 + - - +
25D GLU* 3.0 25.7 + - - +
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Residues in contact with ARG 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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181C LEU 5.0 2.6 + - - -
184C GLN* 3.4 39.2 + - - +
20D ASP* 3.3 10.1 + - + +
21D ALA* 1.3 77.9 - - - +
23D THR* 1.3 62.5 + - - +
25D GLU* 3.3 7.9 + - + +
26D ILE* 3.0 44.6 + - + +
181D LEU* 4.1 17.9 - - + +
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Residues in contact with THR 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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180C TYR* 6.1 0.7 - - - -
19D ILE* 4.2 9.9 - - + -
20D ASP* 2.7 38.4 + - - +
22D ARG* 1.3 72.6 - - - +
24D MET* 1.3 58.0 + - - +
26D ILE* 3.2 3.6 + - - +
27D HIS* 2.7 43.9 + - + +
177D HIS 3.7 16.8 + - - +
178D ALA* 3.7 25.5 - - - +
179D TYR 5.5 0.5 - - - -
181D LEU* 3.6 25.8 + - - +
182D ASN 4.7 0.2 + - - -
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Residues in contact with MET 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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8D LEU* 4.0 9.2 - - + -
10D TYR* 3.8 20.9 - - + +
12D TYR* 3.4 37.7 - - + +
15D LEU* 3.8 28.3 - - + -
19D ILE* 3.6 29.4 - - + +
20D ASP 3.0 16.2 + - - +
21D ALA 3.7 2.2 - - - +
22D ARG 3.4 0.2 - - - -
23D THR* 1.3 75.8 - - - +
25D GLU* 1.3 62.7 + - - +
27D HIS* 3.8 5.5 - - - +
28D HIS* 3.0 27.0 + - - +
84D PHE* 6.0 0.4 - - - -
85D TRP* 3.8 31.4 - - + -
88D MET* 4.3 1.8 - - + -
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Residues in contact with GLU 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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12D TYR* 3.7 35.6 - - + +
21D ALA 3.0 18.0 + - - +
22D ARG* 3.6 7.3 - - - +
24D MET* 1.3 76.1 - - - +
26D ILE* 1.3 56.8 + - + +
29D THR* 2.7 51.3 + - + +
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Residues in contact with ILE 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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180C TYR* 3.5 22.4 - - + +
184C GLN* 3.7 28.3 - - + +
185C ASN* 3.6 22.7 - - - +
22D ARG* 3.0 41.4 + - + +
23D THR* 4.0 2.7 - - - +
25D GLU* 1.3 77.8 - - + +
27D HIS* 1.3 67.5 + - - +
29D THR* 4.2 4.5 - - - -
30D LYS* 2.9 31.5 + - + -
31D HIS* 3.2 10.1 + - - +
181D LEU* 4.2 7.6 - - + -
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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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180C TYR* 5.1 0.4 + - - -
19D ILE* 6.4 0.2 - - - +
23D THR* 2.7 29.3 + - + +
24D MET* 3.8 5.1 - - - +
26D ILE* 1.3 74.5 - - - +
28D HIS* 1.3 57.0 + - - +
31D HIS* 3.4 11.9 - - + +
32D HIS* 2.9 28.1 + - - +
81D HIS* 3.0 16.3 + + - -
84D PHE* 4.0 18.0 - + - -
85D TRP* 3.5 16.5 - + + -
173D ASP* 2.9 17.3 - - - -
177D HIS* 3.2 15.2 + + - +
178D ALA* 3.8 23.6 + - + -
229D FE 2.2 26.4 - - - -
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Residues in contact with HIS 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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5D LEU* 3.5 31.3 - - + +
6D PRO 2.6 29.5 + - - -
7D GLN* 4.4 3.6 - - - -
8D LEU* 3.4 32.7 - - + +
12D TYR* 3.1 28.3 + + + -
24D MET 3.0 18.9 + - - +
25D GLU 4.0 1.8 - - - +
27D HIS* 1.3 77.8 - - - +
29D THR* 1.3 64.0 + - + +
32D HIS* 3.4 6.2 - - - +
33D GLN 3.3 19.4 + - - -
85D TRP* 3.6 24.2 - - + -
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Residues in contact with THR 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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5D LEU* 4.5 9.4 - - + -
12D TYR* 3.2 28.3 - - + +
25D GLU* 2.7 37.7 + - + +
26D ILE* 4.2 0.5 - - - -
28D HIS* 1.3 76.0 - - - +
30D LYS* 1.3 77.1 + - - +
33D GLN* 3.2 20.2 - - - +
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Residues in contact with LYS 30 (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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185C ASN* 3.7 43.1 - - + +
26D ILE* 2.9 23.5 + - + +
29D THR* 1.3 95.3 + - - +
31D HIS* 1.3 62.5 + - - +
32D HIS 3.6 0.2 - - - -
33D GLN* 3.8 1.3 - - - +
34D THR* 2.8 34.3 + - - -
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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