Contacts of the helix formed by residues 21 - 38 (chain A) in PDB entry 2Y60
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PRO* 5.1 2.9 + - + +
19A GLY 3.6 2.2 - - - -
20A ASP* 1.3 76.7 - - - +
22A GLN* 1.3 63.5 + - - +
23A ALA* 3.5 8.7 + - - +
24A ALA* 3.1 31.8 + - + +
25A LYS* 3.0 25.7 + - - +
27A ARG* 4.7 3.9 + - - -
1334A SO4 5.0 1.2 + - - -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP* 2.6 37.9 + - - +
21A ASP* 1.3 73.1 + - - +
23A ALA* 1.3 57.6 + - - +
25A LYS* 3.1 33.6 + - - +
26A MET* 2.9 33.4 + - + +
162A LEU* 5.4 2.6 - - - +
168A GLU* 4.2 4.2 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.3 7.9 + - - +
22A GLN* 1.3 78.0 - - - +
24A ALA* 1.3 63.1 + - - +
26A MET* 3.1 11.0 + - - +
27A ARG* 3.0 45.2 + - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 4.0 18.6 - - + -
21A ASP* 3.1 29.8 + - + +
23A ALA* 1.3 78.0 - - - +
25A LYS* 1.3 64.6 + - - +
27A ARG* 3.2 16.2 + - - +
28A VAL* 3.0 24.9 + - - +
1334A SO4 3.7 22.1 + - - +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PRO* 3.3 30.7 - - - +
17A LEU* 4.2 23.1 + - + +
19A GLY 3.3 21.5 + - - +
20A ASP* 4.6 0.2 - - - +
21A ASP 3.0 20.1 + - - +
22A GLN* 3.1 33.2 + - - +
24A ALA* 1.3 77.5 - - - +
26A MET* 1.3 56.4 + - - +
28A VAL* 3.2 5.0 + - - +
29A ALA* 2.8 27.9 + - - +
158A LYS* 5.5 2.6 - - - +
162A LEU* 3.9 18.3 - - + +
168A GLU* 2.7 33.3 + - - -
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 2.9 22.1 + - + +
23A ALA* 3.1 10.3 + - - +
25A LYS* 1.3 76.4 - - - +
27A ARG* 1.3 57.3 + - + +
29A ALA* 3.1 7.4 + - + +
30A GLN* 2.8 29.1 + - - +
162A LEU* 4.2 39.9 - - + +
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 4.7 3.8 + - - -
23A ALA* 3.0 35.4 + - - +
24A ALA* 3.2 21.8 + - - +
26A MET* 1.3 73.2 - - + +
28A VAL* 1.3 65.3 + - - +
30A GLN* 3.5 8.9 + - - +
31A GLN* 3.3 30.6 + - - +
1334A SO4 2.6 43.1 + - - +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.9 18.8 - - + -
13A ASP 3.5 21.1 - - - +
14A VAL* 4.5 2.0 - - - -
16A PRO* 3.7 23.8 - - + -
17A LEU* 3.8 30.3 - - + -
24A ALA 3.0 14.9 + - - +
25A LYS 3.6 6.5 - - - +
27A ARG* 1.3 73.1 - - + +
29A ALA* 1.3 67.6 + - - +
31A GLN* 2.9 24.4 + - - +
32A ILE* 3.0 18.0 + - + +
1334A SO4 5.6 2.0 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS 2.8 14.4 + - - +
26A MET* 3.1 13.2 + - + +
28A VAL* 1.3 76.7 - - - +
30A GLN* 1.4 57.1 + - - +
32A ILE* 3.1 6.0 + - - -
33A ASP* 2.8 25.5 + - - +
159A GLY* 3.6 15.4 - - - +
162A LEU* 3.7 14.6 - - + +
163A ALA* 3.4 35.9 - - - +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET 2.8 13.5 + - - +
27A ARG* 3.7 11.1 - - - +
28A VAL 3.2 0.4 - - - -
29A ALA* 1.4 75.3 - - - +
31A GLN* 1.3 71.4 + - - +
33A ASP* 3.3 12.0 + - + +
34A ALA* 2.9 41.1 + - - +
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 5.5 1.2 - - - +
11A LYS 4.6 3.3 - - - +
12A ILE* 3.6 40.3 - - + +
13A ASP* 5.0 3.1 + - - +
27A ARG* 3.3 22.3 + - - +
28A VAL* 2.9 21.9 + - - +
30A GLN* 1.3 89.7 - - - +
32A ILE* 1.4 57.1 + - - +
34A ALA* 3.3 5.4 + - - +
35A ALA* 3.0 29.8 + - - +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.1 11.4 - - + -
14A VAL* 5.4 0.7 - - + -
17A LEU* 4.2 7.6 - - + -
28A VAL* 3.0 25.8 + - + +
29A ALA* 3.1 6.9 + - - +
31A GLN* 1.4 73.6 - - - +
33A ASP* 1.3 58.3 + - - +
35A ALA* 3.3 3.8 + - - +
36A SER* 2.7 37.9 + - - +
42A PHE* 3.9 24.7 - - + -
156A LEU* 4.5 6.5 - - + +
159A GLY* 3.9 27.1 - - - +
160A TYR* 3.6 47.1 - - + +
163A ALA* 4.5 3.8 - - + -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 2.8 13.8 + - - +
30A GLN* 3.4 16.4 + - - +
32A ILE* 1.3 76.9 - - - +
34A ALA* 1.3 64.7 + - - +
36A SER* 3.2 1.7 + - - -
37A ARG* 2.7 65.0 + - - +
163A ALA* 3.9 11.6 - - + +
264A TYR* 3.1 20.9 + - - -
265A TYR* 2.6 31.2 + - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 2.9 32.6 + - - +
31A GLN* 3.7 6.3 - - - +
33A ASP* 1.3 78.2 + - - +
35A ALA* 1.3 64.0 + - - +
37A ARG* 3.3 7.1 + - - +
38A ASP* 3.1 26.1 + - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.1 14.1 - - + +
12A ILE* 4.6 0.2 - - + -
31A GLN 3.0 18.0 + - - +
32A ILE 3.9 2.7 - - - +
34A ALA* 1.3 78.4 - - - +
36A SER* 1.4 60.5 + - - +
38A ASP* 3.2 9.1 + - - -
39A THR 3.6 1.7 + - - -
40A GLY* 2.9 26.6 + - - -
41A PHE 3.7 20.8 - - - +
42A PHE* 3.9 24.5 - - + -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 2.7 23.4 + - - +
33A ASP 3.7 2.5 - - - -
35A ALA* 1.4 76.5 - - - +
37A ARG* 1.3 61.0 + - - +
38A ASP 3.7 1.2 + - - +
40A GLY* 4.1 16.7 + - - -
42A PHE* 5.1 2.5 - - - -
160A TYR* 3.5 25.2 + - - -
253A CYS* 4.6 4.1 - - - -
264A TYR 4.6 0.5 - - - +
265A TYR* 3.6 44.1 - - - -
266A LYS* 4.5 12.0 + - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 2.7 58.9 + - - +
34A ALA* 3.8 6.4 - - - +
35A ALA 3.2 0.2 - - - -
36A SER* 1.3 76.2 - - - +
38A ASP* 1.3 59.9 + - - +
264A TYR* 3.5 37.5 + - + +
265A TYR* 4.0 13.5 - - + -
266A LYS* 4.5 8.4 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.7 29.3 + - - +
10A PRO* 6.1 0.2 - - - +
34A ALA 3.1 16.2 + - - +
35A ALA* 3.2 6.1 + - - +
36A SER 4.5 0.2 - - - +
37A ARG* 1.3 81.4 - - - +
39A THR* 1.3 75.1 + - - +
40A GLY 3.3 1.0 + - - -
266A LYS* 3.8 14.4 + - - -
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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
------------------------------------------------------------
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