Contacts of the helix formed by residues 52 - 65 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50G GLU* 2.9 14.0 + - - +
51G ASN* 1.3 74.4 - - - +
53G GLU* 1.3 76.5 + - + +
54G GLU* 3.2 20.2 - - + +
55G ASN* 3.3 26.1 + - - +
56G ARG* 3.2 29.8 + - - +
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Residues in contact with GLU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G THR* 1.3 77.6 - - + +
54G GLU* 1.3 59.2 + - - +
56G ARG* 3.1 30.0 + - - +
57G ARG 2.9 23.2 + - - -
82G GLU* 3.6 12.9 - - - +
86G GLN* 3.5 15.1 + - - +
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Residues in contact with GLU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G THR* 3.1 14.4 - - + +
53G GLU* 1.3 77.8 - - - +
55G ASN* 1.3 62.7 + - - +
57G ARG* 2.9 36.5 + - - +
58G LEU* 2.7 51.5 + - + +
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Residues in contact with ASN 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 4.4 3.8 - - + +
49G VAL* 3.7 17.2 - - + +
50G GLU* 2.5 45.8 + - - +
52G THR* 3.3 21.7 + - - +
53G GLU 3.5 0.2 - - - -
54G GLU* 1.3 79.8 - - - +
56G ARG* 1.3 58.3 + - - +
58G LEU* 3.6 18.2 - - - +
59G TYR* 3.0 22.0 + - - +
314G TRP* 3.5 13.7 - - + -
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Residues in contact with ARG 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G VAL* 3.2 34.9 - - - +
40G MET* 3.5 36.8 - - + -
44G LEU* 4.1 6.1 - - + -
51G ASN* 2.8 34.6 + - - +
52G THR 3.2 17.4 + - - +
53G GLU* 3.1 29.2 - - - +
54G GLU 3.0 0.6 - - - -
55G ASN* 1.3 76.1 - - - +
57G ARG* 1.3 67.0 + - - +
59G TYR* 3.1 6.5 + - - +
60G ARG* 2.8 39.9 + - - +
80G PHE* 6.2 0.4 - - - -
82G GLU* 2.8 41.4 + - - +
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Residues in contact with ARG 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G GLU 2.9 9.5 + - - +
54G GLU* 2.9 36.5 + - - +
56G ARG* 1.3 75.1 - - - +
58G LEU* 1.3 87.5 + - - +
60G ARG* 3.4 1.7 + - - +
61G GLN* 2.9 33.0 + - - +
86G GLN* 3.4 34.9 + - + +
87G LYS 3.0 31.8 + - - +
88G ASP* 3.6 9.3 + - - +
89G ASP* 2.9 29.4 + - - +
94G PHE* 3.4 14.0 - - + -
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Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G GLU* 2.7 36.9 + - + +
55G ASN* 3.6 24.9 - - - +
57G ARG* 1.3 99.5 - - - +
59G TYR* 1.3 61.9 + - - +
61G GLN* 3.0 30.4 - - - +
62G VAL* 3.1 12.7 + - - +
89G ASP* 4.4 3.4 - - - +
314G TRP* 4.0 14.6 - - + +
316G GLY 5.9 2.0 - - - +
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Residues in contact with TYR 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G MET* 4.6 20.4 - - + -
44G LEU* 4.9 3.4 - - + -
55G ASN 3.0 15.0 + - - +
56G ARG* 3.1 5.1 + - - +
58G LEU* 1.3 77.2 - - - +
60G ARG* 1.3 80.1 + - - +
62G VAL* 2.9 32.5 + - + +
63G LEU* 3.4 23.1 + - + +
307G GLN* 2.7 56.1 + - - +
310G ALA 4.9 2.0 - - - -
311G LEU* 3.3 43.9 + - + +
314G TRP* 3.6 25.7 - + + -
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Residues in contact with ARG 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ALA* 3.1 24.1 + - - +
35G GLU* 2.6 63.2 + - - +
40G MET* 3.5 24.3 - - - +
56G ARG* 2.8 37.3 + - - +
57G ARG 3.8 3.8 - - - +
59G TYR* 1.3 82.8 - - - +
61G GLN* 1.3 56.6 + - - +
63G LEU* 3.1 10.1 + - - +
64G PHE* 2.9 49.4 + - + -
80G PHE* 4.2 4.9 - - - +
82G GLU* 5.1 0.4 + - - -
83G THR* 3.3 29.1 + - + +
86G GLN* 4.2 3.8 - - - +
94G PHE* 4.1 6.5 - - + -
307G GLN* 4.8 4.4 + - - -
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Residues in contact with GLN 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ARG* 2.9 16.6 + - - +
58G LEU* 3.0 25.1 - - - +
60G ARG* 1.3 75.7 - - - +
62G VAL* 1.3 55.7 + - - +
64G PHE* 4.4 0.7 - - - +
65G SER* 2.6 46.9 + - - +
88G ASP* 3.0 16.4 - - + +
89G ASP* 2.7 59.5 + - - +
94G PHE* 3.8 18.8 - - + -
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Residues in contact with VAL 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G LEU 3.1 15.1 + - - +
59G TYR* 2.9 19.1 + - + +
61G GLN* 1.3 75.9 - - - +
63G LEU* 1.3 66.0 + - + +
65G SER* 3.2 9.7 + - - -
310G ALA* 5.7 0.2 - - + -
314G TRP* 3.9 30.5 - - + +
321G ALA* 3.6 12.8 - - + +
324G ALA* 3.3 31.4 - - + -
325G THR* 2.8 43.1 + - - +
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU* 4.2 18.8 - - + -
33G ALA* 4.4 10.3 - - + -
59G TYR* 3.4 34.1 + - + +
60G ARG* 3.1 10.5 + - - +
61G GLN 3.0 0.4 - - - -
62G VAL* 1.3 78.5 - - + +
64G PHE* 1.3 71.8 + - + +
65G SER 3.1 4.3 - - - -
66G ALA* 3.1 23.7 + - - +
307G GLN* 3.6 38.1 - - + +
310G ALA* 4.6 4.3 - - + -
328G PHE* 3.4 38.8 - - + -
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Residues in contact with PHE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU* 4.3 11.7 - - + -
33G ALA* 4.4 13.9 - - + -
60G ARG* 2.9 32.3 + - + +
61G GLN 4.2 1.3 - - - +
63G LEU* 1.3 77.4 - - + +
65G SER* 1.3 58.0 + - - +
66G ALA* 3.1 6.9 + - - +
77G VAL* 3.6 27.4 - - + -
79G PHE* 3.7 21.3 - + - -
83G THR* 3.6 28.0 - - + -
94G PHE* 3.3 36.3 - + + -
97G THR* 3.6 22.5 - - + +
98G ILE* 3.5 26.7 - - + +
101G LYS* 4.4 2.9 - - - -
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G GLN* 2.6 30.8 + - - +
62G VAL* 3.2 13.0 + - - -
63G LEU 3.1 0.4 - - - -
64G PHE* 1.3 76.5 - - - +
66G ALA* 1.3 67.3 - - - +
67G ASP* 3.5 1.9 + - - +
97G THR* 5.6 0.9 - - - -
325G 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