Contacts of the helix formed by residues 52 - 65 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F GLU* 2.9 14.2 + - - +
51F ASN* 1.3 74.0 - - - +
53F GLU* 1.3 75.8 + - + +
54F GLU* 3.1 20.4 - - + +
55F ASN* 3.3 26.5 + - - +
56F ARG* 3.2 29.7 + - - +
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F THR* 1.3 79.1 - - + +
54F GLU* 1.3 58.9 + - - +
56F ARG* 3.1 30.8 + - - +
57F ARG* 2.9 23.9 + - - +
82F GLU* 3.6 12.3 - - + +
86F GLN* 3.5 14.8 + - - +
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F THR* 3.1 14.4 - - + +
53F GLU* 1.3 78.3 - - - +
55F ASN* 1.3 62.6 + - - +
57F ARG* 2.9 36.8 + - - +
58F LEU* 2.7 51.3 + - + +
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Residues in contact with ASN 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 4.4 4.5 - - + +
49F VAL* 3.7 18.0 - - + +
50F GLU* 2.5 44.7 + - - +
52F THR* 3.3 22.3 + - - +
54F GLU* 1.3 79.2 - - - +
56F ARG* 1.3 57.4 + - - +
58F LEU* 3.6 17.8 - - - +
59F TYR* 3.0 22.3 + - - +
314F TRP* 3.5 13.3 - - + -
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 3.2 35.3 - - - +
40F MET* 3.5 36.8 - - + -
44F LEU* 4.1 5.4 - - + -
51F ASN* 2.8 35.2 + - - +
52F THR 3.2 17.9 + - - +
53F GLU* 3.1 28.5 - - - +
54F GLU 3.0 0.8 - - - -
55F ASN* 1.3 74.8 - - - +
57F ARG* 1.3 66.9 + - - +
59F TYR* 3.1 6.7 + - - +
60F ARG* 2.8 40.2 + - - +
80F PHE* 6.2 0.4 - - - -
82F GLU* 2.8 42.0 + - - +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F GLU 2.9 9.5 + - - +
54F GLU* 2.9 36.2 + - - +
56F ARG* 1.3 75.2 - - - +
58F LEU* 1.3 86.5 + - - +
60F ARG* 3.4 1.3 + - - -
61F GLN* 2.9 33.0 + - - +
86F GLN* 3.4 35.1 + - + +
87F LYS 3.0 31.9 + - - +
88F ASP* 3.6 10.1 + - - +
89F ASP* 2.9 29.7 + - - +
94F PHE* 3.4 13.6 - - + -
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLU* 2.7 37.3 + - + +
55F ASN* 3.6 24.0 - - - +
57F ARG* 1.3 98.9 - - - +
59F TYR* 1.3 62.7 + - - +
61F GLN* 3.0 32.5 + - - +
62F VAL* 3.1 12.4 + - - +
89F ASP* 4.4 3.6 - - - +
314F TRP* 4.0 15.5 - - + +
316F GLY 5.9 2.0 - - - +
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Residues in contact with TYR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F MET* 4.6 20.4 - - + -
44F LEU* 4.9 3.8 - - + -
55F ASN 3.0 15.4 + - - +
56F ARG* 3.7 4.7 - - - +
58F LEU* 1.3 77.7 - - - +
60F ARG* 1.3 79.1 + - - +
62F VAL* 2.9 32.3 + - + +
63F LEU* 3.4 22.4 + - + +
307F GLN* 2.7 57.0 + - - +
310F ALA 4.9 1.8 - - - -
311F LEU* 3.3 45.2 - - + +
314F TRP* 3.6 24.4 - + + -
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Residues in contact with ARG 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ALA* 3.1 24.5 + - - +
35F GLU* 2.6 62.4 + - - +
40F MET* 3.5 24.7 - - - +
56F ARG* 2.8 37.5 + - - +
57F ARG 3.8 3.8 - - - +
59F TYR* 1.3 81.7 - - - +
61F GLN* 1.3 57.3 + - - +
63F LEU* 3.1 10.2 + - - +
64F PHE* 2.9 49.3 + - + -
80F PHE* 4.2 5.3 - - - +
82F GLU* 5.1 0.2 + - - -
83F THR* 3.3 29.7 + - + +
86F GLN* 4.2 2.9 - - - +
94F PHE* 4.1 6.7 - - + -
307F GLN* 4.8 4.4 + - - -
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Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ARG* 2.9 17.0 + - - +
58F LEU* 3.0 24.4 - - - +
59F TYR 3.0 0.2 - - - -
60F ARG* 1.3 74.9 - - - +
62F VAL* 1.3 55.0 + - - +
64F PHE* 4.4 0.7 - - - +
65F SER* 2.6 46.5 + - - +
88F ASP* 3.0 17.2 - - + +
89F ASP* 2.7 59.9 + - - +
94F PHE* 3.8 19.7 - - + -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LEU 3.1 14.6 + - - +
59F TYR* 2.9 19.8 + - + +
61F GLN* 1.3 76.4 - - - +
63F LEU* 1.3 65.6 + - + +
65F SER* 3.2 10.6 + - - -
310F ALA* 5.7 0.7 - - + -
314F TRP* 3.9 29.6 - - + +
321F ALA* 3.6 12.8 - - + +
324F ALA* 3.3 31.2 - - + -
325F THR* 2.8 41.8 + - - +
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 4.2 19.3 - - + -
33F ALA* 4.4 11.4 - - + -
59F TYR* 3.9 33.9 - - + +
60F ARG* 3.1 10.9 + - - +
61F GLN 3.0 0.8 - - - -
62F VAL* 1.3 78.2 - - + +
64F PHE* 1.3 71.1 + - + +
65F SER 3.1 4.3 - - - -
66F ALA* 3.1 23.9 + - - +
307F GLN* 3.6 38.1 - - + +
310F ALA* 4.6 4.5 - - + -
328F PHE* 3.4 40.0 - - + -
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Residues in contact with PHE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 4.3 12.1 - - + -
33F ALA* 4.4 13.9 - - + -
60F ARG* 2.9 32.3 + - + +
61F GLN 4.2 1.3 - - - +
63F LEU* 1.3 76.5 - - + +
65F SER* 1.3 59.2 + - - +
66F ALA* 3.1 7.0 + - - +
77F VAL* 3.6 26.2 - - + -
79F PHE* 3.6 21.1 - + - -
83F THR* 3.6 28.3 - - + -
94F PHE* 3.3 35.0 - + + -
97F THR* 3.6 23.1 - - + +
98F ILE* 3.5 26.5 - - + +
101F LYS* 4.4 2.6 - - - -
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Residues in contact with SER 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F GLN* 2.6 32.1 + - - +
62F VAL* 3.2 13.5 + - - -
63F LEU 3.1 0.2 - - - -
64F PHE* 1.3 74.7 - - - +
66F ALA* 1.3 68.5 + - - +
67F ASP* 3.5 2.1 + - - +
97F THR* 5.6 1.6 - - - -
101F LYS* 5.4 0.2 - - - -
325F THR* 3.8 10.2 + - - +
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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