Contacts of the helix formed by residues 52 - 65 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLU* 2.9 14.2 + - - +
51B ASN* 1.3 73.4 - - - +
53B GLU* 1.3 76.2 + - + +
54B GLU* 3.2 19.7 - - + +
55B ASN* 3.3 26.2 + - - +
56B ARG* 3.2 29.7 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B THR* 1.3 79.1 - - + +
54B GLU* 1.3 58.3 + - - +
56B ARG* 3.1 29.4 + - - +
57B ARG 2.9 23.4 + - - -
82B GLU* 3.6 11.8 - - - +
86B GLN* 3.5 14.8 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B THR* 3.2 13.9 - - + +
53B GLU* 1.3 78.3 - - - +
55B ASN* 1.3 62.8 + - - +
57B ARG* 2.9 36.5 + - - +
58B LEU* 2.7 50.4 + - + +
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.4 4.7 - - + +
49B VAL* 3.7 18.8 - - + +
50B GLU* 2.5 44.9 + - - +
52B THR* 3.3 20.7 + - - +
53B GLU 3.5 0.2 - - - -
54B GLU* 1.3 79.6 - - - +
56B ARG* 1.3 58.2 + - - +
58B LEU* 3.6 18.1 - - - +
59B TYR* 3.0 22.5 + - - +
314B TRP* 3.5 13.4 - - + -
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU 5.5 0.2 - - - -
37B VAL* 3.2 34.7 - - - +
40B MET* 3.5 37.0 - - + -
44B LEU* 4.1 5.6 - - + -
51B ASN* 2.8 36.2 + - - +
52B THR 3.2 18.3 + - - +
53B GLU* 3.1 28.4 - - - +
54B GLU 3.0 0.6 - - - -
55B ASN* 1.3 75.4 - - - +
57B ARG* 1.3 66.8 + - - +
59B TYR* 3.1 7.0 + - - +
60B ARG* 2.8 40.2 + - - +
80B PHE* 6.2 0.2 - - - -
82B GLU* 2.8 41.8 + - - +
86B GLN* 4.6 0.2 - - - -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU 2.9 9.0 + - - +
54B GLU* 2.9 36.7 + - - +
56B ARG* 1.3 75.6 - - - +
58B LEU* 1.3 87.0 + - - +
60B ARG* 3.4 1.7 + - - -
61B GLN* 2.9 33.4 + - - +
86B GLN* 3.4 33.8 + - + +
87B LYS 3.0 31.7 + - - +
88B ASP* 3.6 9.5 + - - +
89B ASP* 2.9 30.2 + - - +
94B PHE* 3.4 14.4 - - + -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU* 2.7 35.5 + - + +
55B ASN* 3.6 24.5 - - - +
57B ARG* 1.3 98.9 - - - +
59B TYR* 1.3 62.9 + - - +
61B GLN* 3.0 30.9 - - - +
62B VAL* 3.1 12.8 + - - +
89B ASP* 4.4 3.4 - - - +
314B TRP* 4.0 14.8 - - + +
316B GLY 5.9 1.8 - - - +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 4.6 20.0 - - + -
44B LEU* 4.9 3.6 - - + -
55B ASN 3.0 14.6 + - - +
56B ARG* 3.1 5.4 + - - +
58B LEU* 1.3 77.7 - - - +
60B ARG* 1.3 79.2 + - - +
62B VAL* 2.9 32.4 + - + +
63B LEU* 3.4 22.6 + - + +
307B GLN* 2.7 56.9 + - - +
310B ALA 4.9 2.5 - - - -
311B LEU* 3.3 44.9 - - + +
314B TRP* 3.6 25.7 - + + -
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 3.1 24.1 + - - +
35B GLU* 2.6 63.2 + - - +
40B MET* 3.5 24.2 - - - +
56B ARG* 2.8 36.8 + - - +
57B ARG 3.8 3.8 - - - +
59B TYR* 1.3 82.1 - - - +
61B GLN* 1.3 58.1 + - - +
63B LEU* 3.1 10.4 + - - +
64B PHE* 2.9 49.0 + - + -
80B PHE* 4.2 4.9 - - - +
82B GLU* 5.1 0.2 + - - -
83B THR* 3.3 29.4 + - + +
86B GLN* 4.2 3.4 - - - +
94B PHE* 4.1 6.5 - - + -
307B GLN* 4.8 4.9 + - - -
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 2.9 18.1 + - - +
58B LEU* 3.0 24.6 - - - +
59B TYR 3.0 0.2 - - - -
60B ARG* 1.3 75.1 - - - +
62B VAL* 1.3 56.2 + - - +
64B PHE* 4.4 1.1 - - - +
65B SER* 2.6 46.9 + - - +
88B ASP* 3.0 17.4 - - + +
89B ASP* 2.7 58.9 + - - +
94B PHE* 3.8 18.6 - - + -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU 3.1 14.6 + - - +
59B TYR* 2.9 20.0 + - + +
61B GLN* 1.3 75.3 - - - +
63B LEU* 1.3 64.9 + - + +
65B SER* 3.2 10.5 + - - -
310B ALA* 5.7 0.7 - - + -
314B TRP* 3.9 30.5 - - + +
321B ALA* 3.6 12.3 - - + +
324B ALA* 3.3 31.6 - - + -
325B THR* 2.8 43.1 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.2 18.8 - - + -
33B ALA* 4.4 11.4 - - + -
59B TYR* 3.9 33.4 - - + +
60B ARG* 3.1 10.7 + - - +
61B GLN 3.0 0.4 - - - -
62B VAL* 1.3 78.3 - - + +
64B PHE* 1.3 70.3 + - + +
65B SER 3.1 3.8 - - - -
66B ALA* 3.1 24.4 + - - +
307B GLN* 3.6 38.4 - - + +
310B ALA* 4.6 4.3 - - + -
328B PHE* 3.4 39.0 - - + -
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.3 11.7 - - + -
33B ALA* 4.4 13.7 - - + -
60B ARG* 2.9 31.4 + - + +
61B GLN* 4.2 1.6 - - - +
63B LEU* 1.3 77.6 - - + +
65B SER* 1.3 59.1 + - - +
66B ALA* 3.1 6.9 + - - +
77B VAL* 3.6 26.5 - - + -
79B PHE* 3.7 21.5 - + - -
83B THR* 3.6 28.0 - - + -
94B PHE* 3.3 35.7 - + + +
97B THR* 3.6 23.4 - - + +
98B ILE* 3.5 26.4 - - + +
101B LYS* 4.4 2.6 - - - -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 2.6 31.8 + - - +
62B VAL* 3.2 13.9 + - - -
63B LEU 3.1 0.2 - - - -
64B PHE* 1.3 74.0 - - - +
66B ALA* 1.3 67.8 + - - +
67B ASP* 3.5 2.3 + - - +
97B THR* 5.6 1.6 - - - -
325B THR* 3.8 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