Contacts of the helix formed by residues 52 - 65 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 2.9 13.6 + - - +
51A ASN* 1.3 73.8 - - - +
53A GLU* 1.3 77.9 + - + +
54A GLU* 3.2 20.6 - - + +
55A ASN* 3.3 26.4 + - - +
56A ARG* 3.2 28.7 + - - +
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Residues in contact with GLU 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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52A THR* 1.3 77.6 - - + +
54A GLU* 1.3 59.0 + - - +
56A ARG* 3.1 29.6 + - - +
57A ARG* 2.9 24.3 + - - +
82A GLU* 3.6 11.0 - - - +
86A GLN* 3.5 13.9 + - - +
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Residues in contact with GLU 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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52A THR* 3.2 13.7 - - + +
53A GLU* 1.3 77.8 - - - +
55A ASN* 1.3 61.7 + - - +
57A ARG* 2.9 36.6 + - - +
58A LEU* 2.7 50.3 + - + +
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Residues in contact with ASN 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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44A LEU* 4.4 5.3 - - + +
49A VAL* 3.7 17.3 - - + +
50A GLU* 2.5 44.3 + - - +
52A THR* 3.3 21.4 + - - +
53A GLU 3.5 0.4 - - - -
54A GLU* 1.3 80.7 - - - +
56A ARG* 1.3 56.4 + - - +
58A LEU* 3.6 18.7 - - - +
59A TYR* 3.0 21.7 + - - +
314A TRP* 3.5 13.9 - - + -
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Residues in contact with ARG 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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37A VAL* 3.2 35.8 - - - +
40A MET* 3.5 36.6 - - + -
44A LEU* 4.1 5.4 - - + -
51A ASN* 2.8 34.5 + - - +
52A THR 3.2 16.4 + - - +
53A GLU* 3.1 29.4 - - - +
54A GLU 3.0 0.6 - - - -
55A ASN* 1.3 74.5 - - - +
57A ARG* 1.3 67.3 + - - +
59A TYR* 3.1 7.3 + - - +
60A ARG* 2.8 39.4 + - - +
80A PHE* 6.2 0.7 - - - -
82A GLU* 2.8 41.8 + - - +
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Residues in contact with ARG 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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53A GLU 2.9 9.5 + - - +
54A GLU* 2.9 37.3 + - - +
56A ARG* 1.3 74.8 - - - +
58A LEU* 1.3 86.5 + - - +
60A ARG* 3.4 1.7 + - - -
61A GLN* 2.9 33.0 + - - +
86A GLN* 3.4 34.2 + - + +
87A LYS 3.0 32.5 + - - +
88A ASP* 3.6 10.1 + - - +
89A ASP* 2.9 29.3 + - - +
94A PHE* 3.4 14.4 - - + -
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Residues in contact with LEU 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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54A GLU* 2.7 37.6 + - + +
55A ASN* 3.6 23.3 - - - +
57A ARG* 1.3 98.2 - - - +
59A TYR* 1.3 62.3 + - - +
61A GLN* 3.0 31.9 - - - +
62A VAL* 3.1 12.9 + - - +
89A ASP* 4.4 2.9 - - - +
314A TRP* 4.0 15.5 - - + -
316A GLY 5.9 1.3 - - - +
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Residues in contact with TYR 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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40A MET* 4.6 20.6 - - + -
44A LEU* 4.9 3.6 - - + -
55A ASN 3.0 14.4 + - - +
56A ARG* 3.7 4.9 - - - +
58A LEU* 1.3 77.9 - - - +
60A ARG* 1.3 79.4 + - - +
62A VAL* 2.9 32.2 + - + +
63A LEU* 3.4 22.8 + - + +
307A GLN* 2.7 55.5 + - - +
310A ALA 4.9 2.2 - - - -
311A LEU* 3.3 44.3 + - + +
314A TRP* 3.6 24.4 - + + -
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Residues in contact with ARG 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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33A ALA* 3.1 24.0 + - - +
35A GLU* 2.6 62.4 + - - +
40A MET* 3.5 24.4 - - - +
56A ARG* 2.8 38.6 + - - +
57A ARG 3.8 3.8 - - - +
59A TYR* 1.3 82.1 - - - +
61A GLN* 1.3 57.6 + - - +
63A LEU* 3.1 10.4 + - - +
64A PHE* 2.9 49.7 + - + -
80A PHE* 4.2 4.8 - - - +
82A GLU* 5.1 0.4 + - - -
83A THR* 3.3 29.8 + - + +
86A GLN* 4.2 2.9 - - - +
94A PHE* 4.1 6.3 - - + -
307A GLN* 4.8 4.6 + - - -
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Residues in contact with GLN 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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57A ARG* 2.9 16.9 + - - +
58A LEU* 3.0 23.7 - - - +
60A ARG* 1.3 75.5 - - - +
62A VAL* 1.3 54.3 + - - +
64A PHE* 4.4 0.4 - - - +
65A SER* 2.6 47.0 + - - +
88A ASP* 3.0 16.2 - - + +
89A ASP* 2.7 59.8 + - - +
94A PHE* 3.8 19.3 - - + -
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Residues in contact with VAL 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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58A LEU 3.1 14.6 + - - +
59A TYR* 2.9 20.1 + - + +
61A GLN* 1.3 75.3 - - - +
63A LEU* 1.3 66.4 + - + +
65A SER* 3.2 10.3 + - - -
310A ALA* 5.7 0.4 - - + -
314A TRP* 3.9 29.8 - - + +
321A ALA* 3.6 13.0 - - + +
324A ALA* 3.3 31.6 - - + -
325A THR* 2.8 41.4 + - - +
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Residues in contact with LEU 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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31A LEU* 4.2 18.6 - - + -
33A ALA* 4.4 10.8 - - + -
59A TYR* 3.9 34.3 - - + +
60A ARG* 3.1 10.7 + - - +
61A GLN 3.0 0.6 - - - -
62A VAL* 1.3 77.9 - - + +
64A PHE* 1.3 69.5 + - + +
65A SER 3.1 3.8 - - - -
66A ALA* 3.1 24.3 + - - +
307A GLN* 3.6 39.0 - - + +
310A ALA* 4.6 4.0 - - + -
328A PHE* 3.4 40.0 - - + -
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Residues in contact with PHE 64 (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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31A LEU* 4.3 11.7 - - + -
33A ALA* 4.4 14.1 - - + -
60A ARG* 2.9 31.6 + - + +
61A GLN 4.2 1.3 - - - +
63A LEU* 1.3 76.6 - - + +
65A SER* 1.3 58.1 + - - +
66A ALA* 3.1 7.0 + - - +
77A VAL* 3.6 26.9 - - + -
79A PHE* 3.7 20.6 - + - -
83A THR* 3.6 28.7 - - + -
94A PHE* 3.3 35.9 - + + -
97A THR* 3.6 23.2 - - + +
98A ILE* 3.5 26.4 - - + +
101A LYS* 4.4 2.8 - - - -
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Residues in contact with SER 65 (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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61A GLN* 2.6 32.0 + - - +
62A VAL* 3.2 13.0 + - - -
63A LEU 3.1 0.2 - - - -
64A PHE* 1.3 75.9 - - - +
66A ALA* 1.3 67.3 + - - +
67A ASP* 3.5 2.4 + - - +
97A THR* 5.6 1.1 - - - -
325A 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