Contacts of the helix formed by residues 51 - 61 (chain A) in PDB entry 1T2K
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 PHE 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS 3.8 15.7 - - - -
41A GLY* 3.7 28.7 - - - -
46A ALA* 4.9 11.7 - - + -
47A GLN 4.3 6.3 - - - -
48A GLN* 2.4 28.6 + - + +
50A ASP* 1.3 101.0 - - + -
52A GLY* 1.3 57.1 + - - +
53A ILE* 3.3 3.4 - - - -
54A PHE* 3.6 25.4 - + + -
55A GLN* 2.7 34.8 + - + +
73A LEU* 3.4 61.9 - - + -
76A TRP* 4.8 1.8 - - + -
77A LYS* 4.3 14.8 - - + -
12E G 4.2 3.1 - - - -
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Residues in contact with GLY 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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21A LEU* 4.0 15.6 - - - +
48A GLN* 2.9 11.4 + - - -
49A GLU* 3.8 7.3 + - - -
50A ASP 3.7 1.4 - - - -
51A PHE* 1.3 77.2 - - - +
53A ILE* 1.3 61.2 + - - +
55A GLN* 3.7 7.6 - - - +
56A ALA* 2.7 31.4 + - - +
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Residues in contact with ILE 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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11A TRP* 4.3 11.9 - - + -
12A LEU* 4.3 17.5 - - + -
15A GLN* 5.5 2.5 - - + -
21A LEU* 4.2 8.2 - - + +
24A VAL* 3.4 32.8 - - + -
36A ILE* 3.8 23.3 - - + -
37A PRO* 4.0 19.7 - - + +
49A GLU 5.3 1.1 - - - +
50A ASP 4.9 0.2 - - - -
51A PHE* 4.2 3.8 - - - -
52A GLY* 1.3 78.9 - - - +
54A PHE* 1.3 77.8 + - + +
56A ALA* 3.8 3.8 - - - +
57A TRP* 3.0 27.7 + - - +
80A PHE* 4.1 26.0 - - + -
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Residues in contact with PHE 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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36A ILE* 3.9 6.1 - - + -
37A PRO 3.4 20.4 - - - -
38A TRP* 3.7 30.5 - + - -
50A ASP 3.8 16.2 - - - -
51A PHE* 3.3 26.2 + + + +
53A ILE* 1.3 79.5 - - + +
55A GLN* 1.3 61.9 + - - +
57A TRP* 4.2 3.6 - - - +
58A ALA* 3.3 19.6 + - - +
76A TRP* 3.5 33.0 - - + +
77A LYS* 3.6 38.8 - - + +
80A PHE* 3.0 43.7 - + + -
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Residues in contact with GLN 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 GLN* 4.0 24.8 - - - +
51A PHE 2.7 18.5 + - - +
52A GLY* 3.7 5.3 - - - +
54A PHE* 1.3 77.0 - - - +
56A ALA* 1.3 61.1 + - - +
58A ALA* 2.9 4.3 + - - +
59A GLU* 2.8 40.5 + - - +
64A TYR* 3.1 34.5 + - + -
71A PRO* 6.0 0.2 - - - +
76A TRP* 3.4 37.4 - - + -
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Residues in contact with ALA 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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11A TRP* 3.6 18.4 - - + -
15A GLN* 5.3 1.8 - - - +
21A LEU* 4.3 13.9 - - + -
52A GLY 2.7 23.5 + - - +
53A ILE 3.8 2.5 - - - +
55A GLN* 1.3 75.0 - - - +
57A TRP* 1.3 54.0 + - - +
59A GLU* 3.2 12.0 + - - +
60A ALA* 2.7 35.7 + - - +
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Residues in contact with TRP 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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5A LYS* 5.3 1.3 - - - -
6A PRO* 3.3 28.3 - - + -
7A ARG 4.1 2.5 - - - -
8A ILE* 3.4 46.8 - - + +
11A TRP* 3.3 50.8 - + + -
53A ILE 3.0 12.9 + - - +
54A PHE* 4.2 3.8 - - - +
56A ALA* 1.3 77.1 - - - +
58A ALA* 1.3 66.1 + - + +
60A ALA* 3.3 3.6 - - + +
61A THR* 2.9 50.1 + - + +
76A TRP 5.5 0.7 - - - -
79A ASN* 5.3 4.2 + - + +
80A PHE* 4.6 29.1 - + + +
83A ALA* 5.2 1.2 - - + +
15F G 3.7 12.1 - - - -
16F T 3.0 27.4 + - - -
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Residues in contact with ALA 58 (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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54A PHE 3.3 13.8 + - - +
55A GLN 2.9 9.5 + - - +
57A TRP* 1.3 85.4 - - + +
59A GLU* 1.3 62.4 + - - +
61A THR* 3.4 5.2 + - - -
62A GLY 3.3 1.7 + - - -
63A ALA* 3.0 32.0 + - + -
64A TYR* 3.2 13.0 + - + +
76A TRP* 3.6 28.7 - - + +
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Residues in contact with GLU 59 (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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55A GLN* 2.8 32.3 + - - +
56A ALA* 3.6 12.3 - - - +
58A ALA* 1.3 77.2 - - - +
60A ALA* 1.3 62.2 + - - +
62A GLY* 3.0 14.0 + - - -
64A TYR* 3.2 43.6 + - + +
66A PRO* 3.9 18.3 - - + +
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Residues in contact with ALA 60 (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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6A PRO* 3.9 20.9 - - + +
11A TRP* 3.7 27.8 - - + +
56A ALA 2.7 17.8 + - - +
57A TRP* 3.3 13.7 - - + +
58A ALA 3.2 0.2 - - - -
59A GLU* 1.3 79.1 - - - +
61A THR* 1.3 61.2 + - - +
62A GLY 3.6 0.2 + - - -
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Residues in contact with THR 61 (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 LYS* 3.7 32.5 - - + +
6A PRO* 4.7 5.2 - - + -
57A TRP* 2.9 56.6 + - + +
58A ALA* 3.4 7.4 + - - -
60A ALA* 1.3 77.2 - - - +
62A GLY* 1.3 60.9 + - - +
63A ALA* 3.8 11.8 + - - +
16F T 3.7 11.4 + - - +
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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
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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