Contacts of the helix formed by residues 20 - 30 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLU* 3.5 15.5 - - - +
19B ILE* 1.3 75.2 - - - +
21B ALA* 1.3 65.0 + - - +
22B ARG* 3.9 9.1 - - + +
23B THR* 2.7 44.3 + - - +
24B MET* 3.1 21.0 + - - +
179B TYR* 6.0 0.7 - - - -
181B LEU* 3.8 11.2 - - - +
182B ASN* 3.2 37.4 + - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.3 28.8 - - + +
13B ASP* 3.8 18.2 - - + -
16B GLU* 2.9 19.4 + - - +
19B ILE 3.7 0.2 + - - -
20B ASP* 1.3 69.6 - - - +
22B ARG* 1.3 66.4 + - - +
24B MET* 3.3 2.4 + - - +
25B GLU* 3.0 25.2 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU 5.2 1.6 + - - -
184A GLN* 3.2 40.2 + - - +
20B ASP* 3.3 9.7 + - + +
21B ALA* 1.3 77.8 - - - +
23B THR* 1.3 63.9 + - - +
25B GLU* 3.3 6.4 + - + +
26B ILE* 3.0 40.6 + - + +
181B LEU* 3.7 18.8 - - + +
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Residues in contact with THR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR* 6.1 1.8 - - + -
19B ILE* 4.2 11.0 - - + -
20B ASP* 2.7 37.9 + - - +
21B ALA 3.3 0.2 - - - -
22B ARG* 1.3 76.1 - - - +
24B MET* 1.3 53.9 + - - +
26B ILE* 3.9 2.9 - - - +
27B HIS* 2.7 45.6 + - + +
177B HIS 3.7 15.3 + - - +
178B ALA* 3.7 26.4 - - - +
179B TYR 5.6 0.5 - - - -
181B LEU* 3.4 25.9 + - - +
182B ASN 4.8 0.2 + - - -
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.9 19.1 - - + -
10B TYR* 3.9 15.9 - - + -
12B TYR* 3.4 35.6 - - + +
15B LEU* 3.9 19.1 - - + -
19B ILE* 3.6 29.6 - - + +
20B ASP 3.1 16.7 + - - +
21B ALA 3.3 4.0 + - - +
23B THR* 1.3 76.3 - - - +
25B GLU* 1.3 56.0 + - - +
27B HIS* 3.7 6.0 - - - +
28B HIS* 2.9 32.6 + - - +
84B PHE* 5.9 0.7 - - - -
85B TRP* 3.6 36.6 - - + -
88B MET* 4.3 1.1 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.6 41.0 - - + +
21B ALA 3.0 16.9 + - - +
22B ARG* 3.8 6.4 - - - +
23B THR 3.3 0.2 - - - -
24B MET* 1.3 72.5 - - - +
26B ILE* 1.3 57.7 + - + +
28B HIS* 3.3 0.3 + - - -
29B THR* 2.7 53.5 + - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.4 25.1 - - - +
184A GLN* 3.8 28.9 - - + +
185A ASN* 3.9 20.0 - - - +
22B ARG* 3.0 40.3 + - + +
23B THR* 3.9 2.9 - - - +
25B GLU* 1.3 77.0 - - + +
27B HIS* 1.3 64.0 + - - +
29B THR* 4.1 4.7 - - - -
30B LYS* 2.9 32.2 + - + +
31B HIS* 3.2 8.5 + - + +
181B LEU* 4.2 7.9 - - + -
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Residues in contact with HIS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 5.2 0.4 + - - -
19B ILE* 6.3 0.4 - - - +
23B THR* 2.7 29.9 + - + +
24B MET* 3.7 6.4 - - - +
26B ILE* 1.3 72.6 - - - +
28B HIS* 1.3 57.6 + - - +
31B HIS* 3.4 11.4 - - + +
32B HIS* 3.0 28.1 + - - +
81B HIS* 3.0 14.4 + + - -
84B PHE* 3.8 22.2 - + - -
85B TRP* 3.5 17.3 - + + -
173B ASP* 2.8 16.8 + - - -
177B HIS* 3.3 15.2 + + - +
178B ALA* 3.9 20.2 + - + +
229B FE 2.2 27.5 - - - -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.5 30.9 - - + +
6B PRO 2.7 29.5 + - - -
7B GLN* 4.7 2.0 - - - -
8B LEU* 3.3 33.3 - - + +
12B TYR* 2.9 30.5 + + + -
24B MET 2.9 18.5 + - - +
25B GLU 3.8 1.3 - - - +
27B HIS* 1.3 77.4 - - - +
29B THR* 1.3 63.1 + - + +
32B HIS* 3.4 5.9 - - - +
33B GLN 3.3 19.1 + - - -
85B TRP* 3.7 24.4 - - + -
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.5 7.2 - - + -
12B TYR* 3.2 28.9 - - + +
25B GLU* 2.7 41.6 + - + +
26B ILE* 4.1 0.3 - - - -
28B HIS* 1.3 75.9 - - + +
30B LYS* 1.3 81.0 + - - +
33B GLN* 3.1 22.0 - - - +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.7 41.7 - - + +
26B ILE* 2.9 25.5 + - + +
29B THR* 1.3 99.4 + - - +
31B HIS* 1.3 58.0 + - - +
33B GLN* 3.8 1.3 - - - +
34B THR* 2.8 38.7 + - - -
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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