Contacts of the helix formed by residues 45 - 54 (chain A) in PDB entry 2YZ2
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 GLY 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.5 21.8 - - - -
23A LEU* 3.6 5.0 - - - +
43A GLY* 3.1 7.3 + - - +
44A SER* 1.3 77.4 - - - +
46A LYS* 1.3 63.8 + - - +
47A SER 3.3 2.2 - - - -
48A THR* 3.1 10.6 + - - -
49A LEU* 2.9 24.9 + - - +
211A LEU* 3.6 4.9 - - - -
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Residues in contact with LYS 46 (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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38A VAL* 3.5 23.7 - - + +
39A ALA* 3.6 19.3 - - - +
40A GLY 3.0 28.1 + - - +
41A ASN 3.3 14.7 + - - +
42A THR* 4.0 8.3 + - - +
43A GLY 5.2 0.6 - - - +
44A SER* 3.4 9.5 - - - +
45A GLY* 1.3 78.3 - - - +
47A SER* 1.3 67.9 + - - +
49A LEU* 3.6 3.6 - - - +
50A LEU* 3.5 23.0 + - - +
164A GLU* 5.0 4.0 + - - -
194A ILE* 3.3 19.5 - - + -
195A SER* 3.7 6.5 - - - +
196A HIS* 3.6 27.2 + - - +
211A LEU* 3.5 11.3 - - + +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY 3.3 0.6 - - - -
46A LYS* 1.3 83.7 + - - +
48A THR* 1.3 60.2 + - - +
50A LEU* 3.1 3.3 + - - +
51A GLN* 2.9 44.5 + - - +
82A ILE* 5.7 0.2 - - - +
85A GLN* 5.4 2.8 + - - -
163A ASP* 3.6 26.4 + - - -
194A ILE* 4.4 13.5 - - - +
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Residues in contact with THR 48 (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 HIS* 4.0 10.3 - - - +
12A PHE* 3.4 36.2 - - + -
22A ALA* 3.9 15.4 - - + +
23A LEU* 3.8 16.6 - - + -
45A GLY* 3.1 9.7 + - - -
47A SER* 1.3 79.1 - - - +
49A LEU* 1.3 56.4 + - - +
51A GLN* 3.2 15.2 + - - +
52A ILE* 3.0 37.2 + - + +
57A ILE* 4.5 3.1 - - + -
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Residues in contact with LEU 49 (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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5A VAL* 4.3 23.8 - - + -
8A VAL* 5.2 3.6 - - + -
23A LEU* 3.6 23.9 - - + +
26A VAL* 4.1 23.3 - - + -
28A LEU* 4.2 20.2 - - + -
38A VAL* 4.7 11.7 - - + -
45A GLY 2.9 15.5 + - - +
46A LYS 3.6 4.7 - - - +
48A THR* 1.3 76.3 - - - +
50A LEU* 1.3 64.2 + - + +
52A ILE* 3.4 7.1 + - + +
53A VAL* 2.9 31.6 + - + +
209A VAL* 5.4 0.9 - - + -
211A LEU* 3.9 29.2 - - + -
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Residues in contact with LEU 50 (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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28A LEU* 5.6 1.3 - - + -
30A ILE* 5.0 5.6 - - + -
38A VAL* 3.8 20.0 - - + -
46A LYS 3.5 11.4 + - - +
47A SER 3.1 3.9 + - - +
49A LEU* 1.3 82.0 - - + +
51A GLN* 1.3 55.8 + - - +
53A VAL* 3.8 19.1 - - + +
54A ALA* 2.8 35.3 + - - +
82A ILE* 3.9 4.8 - - + +
161A ILE* 3.8 15.0 - - + +
192A ILE* 3.7 37.9 - - + -
194A ILE* 3.2 46.7 - - + -
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Residues in contact with GLN 51 (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 PHE* 5.6 0.5 - - - -
47A SER* 2.9 29.9 + - - +
48A THR* 3.4 16.4 + - - +
50A LEU* 1.3 74.7 - - - +
52A ILE* 1.3 61.3 + - - +
54A ALA 3.4 1.2 + - - -
55A GLY 3.2 3.8 + - - -
56A LEU* 2.9 51.1 + - + +
57A ILE* 3.3 32.3 - - + +
82A ILE* 4.4 7.7 - - + +
84A PHE* 5.7 7.3 - - - +
163A ASP* 4.8 5.3 + - - -
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Residues in contact with ILE 52 (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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5A VAL* 6.2 0.2 - - + -
8A VAL* 4.2 8.3 - - + -
10A HIS* 4.1 14.4 - - + -
23A LEU* 3.6 31.4 - - + -
48A THR* 3.0 12.7 + - + +
49A LEU* 3.5 8.1 - - + +
50A LEU 3.3 0.2 - - - -
51A GLN* 1.3 73.8 - - - +
53A VAL* 1.3 59.0 + - + +
55A GLY* 2.8 24.8 + - - -
57A ILE* 3.7 27.5 - - + +
59A PRO* 3.8 38.4 - - + -
64A VAL* 3.6 22.4 - - + +
66A TYR* 3.6 5.4 + - - -
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Residues in contact with VAL 53 (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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3A ILE* 3.8 33.9 - - + -
5A VAL* 3.5 31.4 - - + -
28A LEU* 5.2 0.7 - - + -
30A ILE* 5.1 6.7 - - + -
49A LEU* 2.9 25.8 + - + +
50A LEU* 3.8 20.2 - - + +
52A ILE* 1.3 71.7 - - + +
54A ALA* 1.3 60.8 + - - +
64A VAL* 4.4 6.1 - - + -
66A TYR* 2.6 30.8 + - + -
80A ILE* 3.7 4.1 - - + +
159A ILE* 5.7 1.1 - - + -
161A ILE* 4.3 14.1 - - + -
192A ILE* 5.3 2.0 - - + -
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Residues in contact with ALA 54 (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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50A LEU 2.8 21.6 + - - +
51A GLN 3.9 5.2 - - - +
52A ILE 3.2 0.4 - - - -
53A VAL* 1.3 72.7 - - - +
55A GLY* 1.4 57.6 + - - +
56A LEU* 4.0 3.8 - - + -
76A ILE* 3.5 10.0 - - - +
77A ARG* 2.9 39.0 + - - +
80A ILE* 4.0 13.5 - - + +
82A ILE* 3.9 27.4 - - + -
161A ILE* 4.0 7.9 - - + -
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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