Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 3THY
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.7 3.8 - - - -
46A HIS* 1.3 70.5 - - - +
48A GLU* 1.3 69.3 + - - +
50A ALA* 2.8 20.1 + - - +
51A LEU* 3.2 8.9 + - - +
75A LEU* 3.7 12.5 - - - +
76A GLN* 2.9 32.9 + - - +
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Residues in contact with GLU 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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29A LYS* 3.2 27.7 + - - +
30A PRO 5.0 0.2 - - - -
31A THR* 3.1 38.5 + - - +
46A HIS 3.5 1.0 + - - -
47A GLY* 1.3 67.9 - - - -
49A ASP* 1.3 65.8 - - - +
51A LEU* 3.0 27.6 + - + +
52A LEU* 3.0 12.8 + - - +
55A ARG* 4.7 1.7 + - - -
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Residues in contact with ASP 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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23A PHE* 6.0 1.0 - - - -
29A LYS* 2.9 41.3 + - - -
31A THR 4.6 1.7 - - - +
34A VAL* 3.6 31.5 - - + +
35A ARG* 3.0 22.7 + - - +
45A ALA* 3.9 15.2 - - + +
46A HIS 3.4 10.7 + - - +
47A GLY 3.0 0.8 + - - -
48A GLU* 1.3 77.4 - - - +
50A ALA* 1.3 66.2 + - - +
52A LEU* 3.1 10.5 + - - +
53A ALA* 2.8 25.3 + - - +
88A PHE* 5.0 1.7 - - - -
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Residues in contact with ALA 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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45A ALA* 3.7 17.9 - - - +
46A HIS* 3.7 4.3 + - - +
47A GLY 2.8 16.4 + - - +
49A ASP* 1.3 74.7 - - - +
51A LEU* 1.3 62.3 + - - +
53A ALA* 3.3 0.3 + - - +
54A ALA* 3.0 18.4 + - - +
64A ILE* 4.9 0.7 - - - -
76A GLN* 3.3 37.5 - - + +
77A SER* 3.7 4.7 - - - +
78A VAL* 3.3 22.7 - - + +
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Residues in contact with LEU 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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47A GLY 3.7 8.7 - - - +
48A GLU* 3.0 17.4 + - + +
50A ALA* 1.3 76.0 - - - +
52A LEU* 1.3 58.5 + - - +
54A ALA* 2.9 23.1 + - - +
55A ARG* 3.0 40.0 + - - +
61A GLN* 4.4 11.3 - - - +
64A ILE* 3.5 24.9 - - + -
76A GLN* 3.7 30.3 - - + +
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Residues in contact with LEU 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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31A THR* 5.5 1.6 - - + +
34A VAL* 4.0 19.1 - - + -
48A GLU 3.0 11.0 + - - +
49A ASP* 3.1 12.5 + - - +
51A LEU* 1.3 76.5 - - - +
53A ALA* 1.3 56.8 + - - +
55A ARG* 3.1 24.4 + - - +
56A GLU* 2.9 49.0 + - + +
88A PHE* 4.1 10.1 - - + -
92A LEU* 4.0 11.9 - - + -
96A ARG* 4.1 16.2 - - - +
98A TYR* 3.9 28.3 - - + +
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Residues in contact with ALA 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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45A ALA* 4.6 9.0 - - + -
49A ASP 2.8 18.3 + - - +
50A ALA 3.6 5.2 - - - +
52A LEU* 1.3 73.5 - - - +
54A ALA* 1.3 60.6 + - - +
57A VAL* 3.2 28.3 + - + +
58A PHE* 3.4 7.0 + - + -
78A VAL* 4.5 14.6 - - + -
80A LEU* 4.7 8.3 - - + -
88A PHE* 3.7 30.7 - - + -
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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 ALA 3.0 12.0 + - - +
51A LEU 2.9 12.4 + - - +
53A ALA* 1.3 77.4 - - - +
55A ARG* 1.3 58.5 + - - +
58A PHE* 3.6 1.5 - - - -
59A LYS 2.9 23.1 + - - -
60A THR 3.0 31.7 + - - +
61A GLN* 3.8 14.4 - - - +
63A VAL* 4.0 11.7 - - + -
64A ILE* 4.0 16.8 - - + -
78A VAL* 4.6 0.7 - - + -
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Residues in contact with ARG 55 (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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48A GLU 4.7 1.4 + - - -
51A LEU* 3.0 40.4 + - - +
52A LEU* 3.4 36.0 - - - +
54A ALA* 1.3 79.1 - - - +
56A GLU* 1.3 68.7 + - - +
59A LYS* 2.9 36.5 + - - +
61A GLN* 4.8 13.3 + - - +
349B GLU* 6.3 2.9 - - - -
351B MET* 6.6 0.2 - - + -
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Residues in contact with GLU 56 (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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52A LEU* 2.9 34.7 + - + +
55A ARG* 1.3 79.7 + - - +
57A VAL* 1.3 61.1 + - - +
59A LYS* 3.1 25.7 + - - +
88A PHE* 3.7 18.8 - - + -
91A ASP* 3.0 25.5 - - - +
92A LEU* 5.4 1.6 - - + -
96A ARG* 2.9 43.2 + - - +
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Residues in contact with VAL 57 (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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53A ALA* 3.2 13.5 + - - +
56A GLU* 1.3 80.6 - - - +
58A PHE* 1.3 88.6 + - + +
59A LYS* 3.5 5.5 + - - +
80A LEU* 4.4 6.1 - - + -
84A ASN* 4.1 11.0 - - + +
87A SER* 6.3 1.3 - - - -
88A PHE* 3.3 47.3 - - + +
262B ASN* 5.8 0.2 - - - +
287B ARG* 3.2 39.7 + - - +
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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