Contacts of the helix formed by residues 52 - 65 (chain I) in PDB entry 1XFB
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 52 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50I GLU* 2.9 14.0 + - - +
51I ASN* 1.3 74.2 - - - +
53I GLU* 1.3 76.9 + - + +
54I GLU* 3.2 20.4 - - + +
55I ASN* 3.3 26.1 + - - +
56I ARG* 3.2 29.8 + - - +
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Residues in contact with GLU 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I THR* 1.3 77.8 - - + +
54I GLU* 1.3 59.2 + - - +
56I ARG* 3.1 29.8 + - - +
57I ARG 2.9 23.2 + - - -
82I GLU* 3.6 12.9 - - - +
86I GLN* 3.5 14.9 + - - +
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Residues in contact with GLU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I THR* 3.1 14.1 - - + +
53I GLU* 1.3 77.6 - - - +
55I ASN* 1.3 62.7 + - - +
57I ARG* 2.9 36.9 + - - +
58I LEU* 2.7 51.7 + - + +
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Residues in contact with ASN 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I LEU* 4.4 3.8 - - + +
49I VAL* 3.7 17.0 - - + +
50I GLU* 2.5 45.4 + - - +
52I THR* 3.3 22.1 + - - +
53I GLU 3.5 0.2 - - - -
54I GLU* 1.3 80.7 - - - +
56I ARG* 1.3 58.3 + - - +
58I LEU* 3.6 18.2 - - - +
59I TYR* 3.0 22.0 + - - +
314I TRP* 3.5 13.7 - - + -
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL* 3.2 35.1 - - - +
40I MET* 3.5 36.6 - - + -
44I LEU* 4.1 5.8 - - + -
51I ASN* 2.8 34.6 + - - +
52I THR 3.2 17.4 + - - +
53I GLU* 3.1 29.4 - - - +
54I GLU 3.0 0.8 - - - -
55I ASN* 1.3 76.1 - - - +
57I ARG* 1.3 66.8 + - - +
59I TYR* 3.1 6.9 + - - +
60I ARG* 2.8 39.5 + - - +
80I PHE* 6.2 0.4 - - - -
82I GLU* 2.8 41.3 + - - +
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Residues in contact with ARG 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I GLU 2.9 9.5 + - - +
54I GLU* 2.9 36.8 + - - +
56I ARG* 1.3 74.9 - - - +
58I LEU* 1.3 86.9 + - - +
60I ARG* 3.4 1.7 + - - +
61I GLN* 2.9 32.9 + - - +
86I GLN* 3.4 34.9 - - + +
87I LYS 3.0 31.8 + - - +
88I ASP* 3.6 9.3 + - - +
89I ASP* 2.9 30.1 + - - +
94I PHE* 3.4 14.4 - - + -
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Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I GLU* 2.7 37.4 + - + +
55I ASN* 3.6 23.8 - - - +
57I ARG* 1.3 99.9 - - - +
59I TYR* 1.3 61.7 + - - +
61I GLN* 3.0 31.0 - - - +
62I VAL* 3.1 13.1 + - - +
89I ASP* 4.4 3.6 - - - +
314I TRP* 4.0 14.1 - - + +
316I GLY 5.9 2.0 - - - +
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Residues in contact with TYR 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I MET* 4.6 20.0 - - + -
44I LEU* 4.9 3.8 - - + -
55I ASN 3.0 15.2 + - - +
56I ARG* 3.1 5.3 + - - +
58I LEU* 1.3 77.2 - - - +
60I ARG* 1.3 80.4 + - - +
62I VAL* 2.9 32.6 + - + +
63I LEU* 3.4 22.8 + - + +
307I GLN* 2.7 56.1 + - - +
310I ALA 4.9 2.2 - - - -
311I LEU* 3.3 43.8 - - + +
314I TRP* 3.6 25.5 - + + -
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Residues in contact with ARG 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ALA* 3.1 24.0 + - - +
35I GLU* 2.6 63.0 + - - +
40I MET* 3.5 24.3 - - - +
56I ARG* 2.8 37.1 + - - +
57I ARG 3.8 3.8 - - - +
59I TYR* 1.3 83.0 - - - +
61I GLN* 1.3 57.0 + - - +
63I LEU* 3.1 10.3 + - - +
64I PHE* 2.9 49.1 + - + -
80I PHE* 4.2 4.9 - - - +
82I GLU* 5.1 0.4 + - - -
83I THR* 3.3 29.6 + - + +
86I GLN* 4.2 3.8 - - - +
94I PHE* 4.1 6.3 - - + -
307I GLN* 4.8 4.4 + - - -
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Residues in contact with GLN 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I ARG* 2.9 16.6 + - - +
58I LEU* 3.0 25.1 - - - +
60I ARG* 1.3 75.5 - - - +
62I VAL* 1.3 55.2 + - - +
64I PHE* 4.4 0.7 - - - +
65I SER* 2.6 46.9 + - - +
88I ASP* 3.0 16.4 - - + +
89I ASP* 2.7 59.3 + - - +
94I PHE* 3.8 18.8 - - + -
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LEU 3.1 15.1 + - - +
59I TYR* 2.9 18.5 + - + +
61I GLN* 1.3 76.1 - - - +
63I LEU* 1.3 66.0 + - + +
65I SER* 3.2 10.3 + - - -
310I ALA* 5.7 0.2 - - + -
314I TRP* 3.9 30.5 - - + +
321I ALA* 3.6 13.0 - - + +
324I ALA* 3.3 31.4 - - + -
325I THR* 2.8 42.6 + - - +
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Residues in contact with LEU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LEU* 4.2 18.6 - - + -
33I ALA* 4.4 10.3 - - + -
59I TYR* 3.4 34.1 + - + +
60I ARG* 3.1 11.1 + - - +
61I GLN 3.0 0.4 - - - -
62I VAL* 1.3 78.7 - - + +
64I PHE* 1.3 71.3 + - + +
65I SER 3.1 4.3 - - - -
66I ALA* 3.1 23.9 + - - +
307I GLN* 3.6 38.1 - - + +
310I ALA* 4.6 4.3 - - + -
328I PHE* 3.4 39.2 - - + -
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Residues in contact with PHE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LEU* 4.3 11.4 - - + -
33I ALA* 4.4 13.7 - - + -
60I ARG* 2.9 32.7 + - + +
61I GLN 4.2 1.1 - - - +
63I LEU* 1.3 77.0 - - + +
65I SER* 1.3 58.0 + - - +
66I ALA* 3.1 7.1 + - - +
77I VAL* 3.6 27.4 - - + -
79I PHE* 3.6 21.5 - + - -
83I THR* 3.6 27.8 - - + -
94I PHE* 3.3 36.3 - + + -
97I THR* 3.6 22.5 - - + +
98I ILE* 3.5 26.7 - - + +
101I LYS* 4.4 2.9 - - - -
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Residues in contact with SER 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I GLN* 2.6 30.8 + - - +
62I VAL* 3.2 13.0 + - - -
63I LEU 3.1 0.4 - - - -
64I PHE* 1.3 76.1 - - - +
66I ALA* 1.3 66.9 - - - +
67I ASP* 3.5 1.7 + - - +
97I THR* 5.6 0.9 - - - -
325I THR* 3.8 10.0 + - - +
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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