Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 2FDR
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 THR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLY 3.5 3.1 + - - +
49A MSE 1.3 75.9 - - - +
51A TRP* 1.3 65.9 + - - +
52A LYS* 3.6 9.4 + - - +
53A ASN* 3.1 36.4 + - - +
54A ILE* 3.0 22.7 + - - +
171A HIS* 6.4 1.8 - - + -
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Residues in contact with TRP 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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26A GLU* 3.6 60.8 + - + +
29A LEU* 4.1 20.9 - - + -
30A LEU* 3.8 17.3 - - + -
49A MSE 3.9 0.4 + - - -
50A THR* 1.3 72.7 - - - +
52A LYS* 1.3 62.4 + - - +
54A ILE* 3.9 26.4 - - + +
55A LEU* 3.1 55.7 + - + +
70A LEU* 3.0 27.3 + - + -
71A LEU* 4.0 16.6 - - + -
74A SER* 3.1 27.6 - - - +
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Residues in contact with LYS 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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50A THR* 3.1 9.3 + - - +
51A TRP* 1.3 79.6 - - - +
53A ASN* 1.3 65.3 + - - +
55A LEU* 3.4 10.4 + - - +
56A LEU* 3.2 40.5 + - + +
71A LEU* 4.0 31.9 - - + +
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Residues in contact with ASN 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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49A MSE 3.3 25.0 - - + +
50A THR* 3.1 27.9 + - - +
52A LYS* 1.3 81.7 - - - +
54A ILE* 1.3 60.2 + - - +
56A LEU* 3.3 17.8 + - - +
57A GLN* 2.8 24.4 + - - +
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Residues in contact with ILE 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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26A GLU* 3.9 21.8 - - - +
30A LEU* 4.0 17.9 - - + -
42A MSE 4.0 4.3 - - + -
46A PHE* 3.6 44.6 - - + +
49A MSE 3.7 27.1 - - + +
50A THR 3.0 22.6 + - - +
51A TRP* 3.6 26.0 - - + +
53A ASN* 1.3 75.1 - - - +
55A LEU* 1.3 58.4 + - - +
57A GLN* 3.2 4.3 + - - +
58A VAL* 2.9 35.2 + - + +
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Residues in contact with LEU 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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30A LEU* 3.9 7.0 - - + -
51A TRP* 3.1 51.3 + - + +
52A LYS* 3.7 4.7 - - - +
53A ASN 3.3 0.2 - - - -
54A ILE* 1.3 75.4 - - - +
56A LEU* 1.3 58.5 + - + +
58A VAL* 3.4 1.5 + - - +
59A GLU* 3.1 26.9 + - - +
66A LEU* 3.3 38.6 - - + +
70A LEU* 3.5 27.8 - - + -
71A LEU* 3.3 34.1 - - + -
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Residues in contact with LEU 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 LYS* 3.2 29.6 + - + +
53A ASN* 3.5 25.4 - - - +
54A ILE 3.2 0.2 - - - -
55A LEU* 1.3 77.7 - - - +
57A GLN* 1.3 55.5 + - - +
59A GLU* 3.4 25.1 - - - +
60A SER* 2.9 29.7 + - - -
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Residues in contact with GLN 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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45A ARG* 4.6 8.5 + - - +
46A PHE* 3.7 19.2 - - + -
49A MSE 3.3 30.9 - - + +
53A ASN 2.8 16.8 + - - +
54A ILE* 3.2 5.6 + - - +
56A LEU* 1.3 73.3 - - - +
58A VAL* 1.3 59.9 + - - +
60A SER* 3.6 5.8 - - - +
61A GLU* 2.7 65.9 + - + +
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Residues in contact with VAL 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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30A LEU* 4.1 16.8 - - + -
35A TYR* 3.6 39.5 - - + +
46A PHE* 3.8 25.4 - - + -
54A ILE* 2.9 22.7 + - + +
55A LEU 3.8 5.2 - - - +
56A LEU 3.3 0.2 - - - -
57A GLN* 1.3 74.2 - - - +
59A GLU* 1.3 60.7 + - - +
61A GLU* 4.8 3.1 - - - -
62A ALA* 2.8 30.0 + - - +
63A SER 3.4 0.5 + - - -
64A ILE* 3.8 15.2 + - + -
66A LEU* 3.8 13.7 - - + -
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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 LEU 3.1 15.5 + - - +
56A LEU* 3.4 30.6 - - - +
58A VAL* 1.3 76.4 - - - +
60A SER* 1.3 65.6 + - - +
63A SER* 2.8 35.7 + - - +
64A ILE 4.0 18.0 - - - +
66A LEU* 4.0 11.1 + - + +
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Residues in contact with SER 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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56A LEU 2.9 20.1 + - - -
57A GLN* 3.6 9.7 + - - +
59A GLU* 1.3 81.1 - - - +
61A GLU* 1.3 63.8 + - - +
63A SER* 4.9 1.4 + - - -
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Residues in contact with GLU 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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35A TYR* 4.3 14.6 + - + +
45A ARG* 5.9 0.2 + - - -
46A PHE* 5.0 1.2 - - - -
57A GLN* 2.7 58.6 + - + +
58A VAL* 4.3 2.6 - - - +
60A SER* 1.3 79.9 - - - +
62A ALA* 1.3 61.2 + - + +
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Residues in contact with ALA 62 (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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35A TYR* 4.0 20.0 - - + -
58A VAL 2.8 16.8 + - - +
60A SER 3.6 0.2 - - - -
61A GLU* 1.3 75.9 - - - +
63A SER* 1.3 64.8 + - - +
64A ILE* 3.0 32.7 + - + +
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Residues in contact with SER 63 (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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58A VAL 3.4 0.4 + - - -
59A GLU* 2.8 25.0 + - - +
60A SER 5.3 1.6 + - - -
62A ALA* 1.3 77.9 - - - +
64A ILE* 1.3 65.2 + - - +
65A PRO* 3.2 9.5 - - - +
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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