Contacts of the helix formed by residues 52 - 70 (chain A) in PDB entry 1XHJ
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 PRO 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR 3.6 7.2 - - - +
51A CYS* 1.3 86.5 - - - +
53A SER* 1.3 60.3 + - - +
54A SER 3.4 0.4 - - - +
55A THR* 3.0 31.0 - - - +
56A ILE* 3.1 29.2 + - + +
80A PHE* 5.1 14.1 - - + -
82A GLU* 4.0 10.1 - - + -
83A HIS 3.4 37.0 - - - +
84A HIS* 4.7 4.0 - - - +
85A HIS 5.8 0.2 - - - +
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS 3.4 6.3 + - - -
52A PRO* 1.3 73.1 - - - +
54A SER* 1.3 61.8 + - - +
56A ILE* 3.9 16.9 - - - +
57A THR* 3.3 16.3 + - - -
85A HIS* 6.2 1.2 - - - +
88A HIS 5.0 11.6 + - - -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 5.7 0.9 + - - -
52A PRO* 4.4 0.6 - - - +
53A SER* 1.3 77.8 - - - +
55A THR* 1.3 72.1 + - - +
56A ILE 3.1 2.2 - - - -
57A THR* 3.0 9.7 + - - -
58A LEU* 2.9 23.5 + - - +
83A HIS* 4.8 14.0 + - - -
85A HIS* 5.0 22.5 - - - +
88A HIS* 6.1 0.4 - - - -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.6 29.8 - - + -
52A PRO* 3.0 29.5 - - + +
53A SER 3.6 0.2 - - - -
54A SER* 1.3 78.6 + - - +
56A ILE* 1.3 53.7 + - - +
58A LEU* 4.3 6.7 - - + -
59A LYS* 2.6 39.3 + - + +
80A PHE* 4.3 23.3 - - + -
83A HIS* 3.4 28.9 + - + +
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Residues in contact with ILE 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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52A PRO* 3.1 22.9 + - + +
53A SER* 3.9 14.1 - - - +
54A SER 3.1 0.4 - - - -
55A THR* 1.3 77.7 - - - +
57A THR* 1.3 64.5 + - - +
59A LYS* 3.4 11.0 - - + +
60A ALA* 3.3 21.8 + - - +
80A PHE* 5.8 9.6 - - + -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 3.3 15.2 + - - -
54A SER* 3.0 8.9 + - - -
56A ILE* 1.3 78.4 - - - +
58A LEU* 1.3 65.8 + - - +
60A ALA* 3.4 6.5 + - - +
61A GLY* 3.0 16.8 + - - -
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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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23A LEU* 5.9 6.5 - - + -
26A ASP* 5.6 5.6 - - + -
27A GLY* 3.5 33.7 - - - +
28A GLY 5.0 0.4 - - - +
44A LEU* 4.8 10.1 - - + -
54A SER* 2.9 15.7 + - - +
55A THR* 3.7 8.3 - - + +
57A THR* 1.3 73.6 - - - +
59A LYS* 1.3 59.0 + - - +
61A GLY* 2.7 23.4 + - - +
62A ILE* 2.8 34.8 + - + +
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Residues in contact with LYS 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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44A LEU* 5.7 1.1 - - - +
55A THR* 2.6 24.6 + - + +
56A ILE* 3.4 11.2 - - + +
58A LEU* 1.3 74.7 - - - +
60A ALA* 1.3 65.3 + - - +
62A ILE* 3.3 9.5 + - - +
63A GLU* 3.1 32.0 + - + +
78A GLN* 3.1 54.3 + - - +
80A PHE* 3.4 32.5 - - + -
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Residues in contact with ALA 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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56A ILE 3.3 8.9 + - - +
57A THR* 3.8 8.1 - - - +
58A LEU 3.3 0.2 - - - -
59A LYS* 1.3 81.3 - - - +
61A GLY* 1.3 59.8 + - - +
63A GLU* 3.9 6.0 - - - +
64A ARG* 3.0 43.6 + - + +
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Residues in contact with GLY 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 THR 3.0 10.2 + - - -
58A LEU* 2.7 17.0 + - - -
60A ALA* 1.3 71.0 - - - +
62A ILE* 1.3 62.9 + - - -
64A ARG* 3.4 4.2 + - - +
65A ALA* 3.0 21.9 + - - +
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Residues in contact with ILE 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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23A LEU* 5.5 12.3 - - + -
30A CYS* 6.2 0.9 - - - -
42A LEU* 6.0 2.0 - - + -
44A LEU* 4.1 25.1 - - + -
58A LEU* 2.8 33.0 + - + +
59A LYS* 3.4 11.0 - - - +
61A GLY* 1.3 68.2 - - - -
63A GLU* 1.3 67.3 + - - +
65A ALA* 2.8 8.3 + - + +
66A LEU* 2.7 40.9 + - + +
78A GLN* 3.8 19.7 - - - +
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Residues in contact with GLU 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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42A LEU* 4.7 4.8 - - - +
59A LYS* 3.1 15.9 + - + +
60A ALA* 3.9 8.1 - - - +
62A ILE* 1.3 77.3 - - - +
64A ARG* 1.3 65.0 + - + +
66A LEU* 3.1 9.8 + - - +
67A HIS* 2.9 36.0 + - + +
76A VAL* 3.2 45.8 - - + +
78A GLN* 2.6 38.8 - - - +
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Residues in contact with ARG 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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60A ALA* 3.0 31.2 + - + +
61A GLY* 3.6 4.5 - - - +
63A GLU* 1.3 79.0 - - + +
65A ALA* 1.3 58.8 + - - +
67A HIS* 3.3 7.2 + - - +
68A GLU* 2.8 36.2 + - - +
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Residues in contact with ALA 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 GLY 3.0 13.2 + - - +
62A ILE* 2.8 17.0 + - + +
64A ARG* 1.3 73.5 - - - +
66A LEU* 1.3 56.1 + - + +
68A GLU* 3.5 5.4 - - - +
69A GLU* 2.7 54.8 + - - +
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Residues in contact with LEU 66 (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 VAL* 6.2 1.6 - - + -
42A LEU* 5.3 16.6 - - + -
62A ILE* 2.7 44.8 + - + +
63A GLU* 3.3 19.5 - - - +
65A ALA* 1.3 74.8 - - + +
67A HIS* 1.3 59.0 + - + +
69A GLU* 3.1 5.9 + - - +
70A VAL* 2.6 48.6 + - + +
73A VAL* 5.8 0.7 - - + -
76A VAL* 5.8 2.9 - - + -
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Residues in contact with HIS 67 (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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63A GLU* 2.9 36.1 + - + +
64A ARG* 3.7 7.4 - - - +
66A LEU* 1.3 80.9 - - + +
68A GLU* 1.3 58.1 + - - +
70A VAL 3.0 7.5 - - - +
71A PRO* 2.9 33.8 - - + +
73A VAL* 3.5 33.0 - - + +
74A ILE 5.9 0.9 - - - -
75A GLU* 5.6 3.4 - - - -
76A VAL* 3.4 32.4 - - + +
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Residues in contact with GLU 68 (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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64A ARG* 2.8 21.4 + - - +
65A ALA* 3.5 7.0 - - - +
67A HIS* 1.3 79.6 - - - +
69A GLU* 1.3 62.3 + - + +
70A VAL 3.3 0.9 + - - -
71A PRO* 3.5 14.7 - - - +
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Residues in contact with GLU 69 (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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65A ALA* 2.7 37.5 + - - +
66A LEU* 3.9 4.6 - - - +
68A GLU* 1.3 75.2 - - + +
70A VAL* 1.3 70.9 + - + +
71A PRO* 3.7 3.3 - - - +
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Residues in contact with VAL 70 (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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8A MET* 5.2 13.7 - - + -
66A LEU* 2.6 25.1 + - + +
67A HIS* 3.0 8.3 - - - +
69A GLU* 1.3 87.7 - - + +
71A PRO* 1.3 68.0 - - - +
73A VAL* 3.4 26.6 - - + +
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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