Contacts of the helix formed by residues 48 - 66 (chain A) in PDB entry 1XO2
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TRP* 3.4 15.1 - - - -
46A GLU 5.3 2.9 - - - +
47A VAL* 1.3 75.7 - - - +
49A VAL* 1.3 66.2 + - - +
50A ASP* 3.5 14.3 + - - +
51A ASN* 3.2 38.6 + - - +
52A ARG 3.4 4.3 + - - -
91A LYS* 5.3 5.7 + - - +
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Residues in contact with VAL 49 (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 LEU* 4.3 24.7 - - + +
41A TRP* 5.2 4.5 - - + -
48A THR* 1.3 73.4 - - - +
50A ASP* 1.3 67.4 + - - +
51A ASN 3.0 2.0 - - - -
52A ARG* 2.9 25.8 + - + +
53A THR* 3.0 12.9 + - - +
188A PRO* 3.4 35.7 - - + -
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Residues in contact with ASP 50 (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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48A THR* 3.3 12.1 + - - +
49A VAL* 1.3 83.5 + - - +
51A ASN* 1.3 63.3 + - - +
53A THR* 3.5 9.9 + - - -
54A ILE* 3.2 32.5 + - + +
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Residues in contact with ASN 51 (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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47A VAL* 3.5 10.8 - - + +
48A THR* 3.2 35.1 + - - +
49A VAL 3.0 0.2 - - - -
50A ASP* 1.3 80.6 - - - +
52A ARG* 1.3 57.6 + - - +
54A ILE* 3.4 15.1 + - - +
55A LEU* 2.9 29.8 + - - +
91A LYS* 3.9 25.7 + - - +
94A LEU* 3.5 26.4 - - + +
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Residues in contact with ARG 52 (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 LEU* 3.6 23.7 - - - +
41A TRP* 3.5 44.1 - - + +
48A THR 3.4 2.2 + - - +
49A VAL* 2.9 15.2 + - - +
51A ASN* 1.3 76.9 - - - +
53A THR* 1.3 57.3 + - - +
55A LEU* 3.0 4.6 + - - +
56A LEU* 2.7 65.5 + - + +
77A VAL* 3.5 18.0 - - - +
80A LEU* 4.9 1.4 - - + +
81A ASP* 2.7 37.4 + - - -
185A LEU 4.1 5.7 + - - -
186A ILE 3.8 9.9 + - - -
187A GLN 4.2 0.4 + - - -
188A PRO* 3.8 20.4 - - - +
191A ALA* 3.7 13.9 - - - +
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Residues in contact with THR 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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49A VAL 3.0 10.9 + - - -
50A ASP* 3.7 13.0 - - - -
52A ARG* 1.3 76.5 - - - +
54A ILE* 1.3 59.2 + - - +
56A LEU* 4.5 0.2 - - - -
57A THR* 2.9 28.1 + - - -
186A ILE* 3.8 20.9 - - + +
187A GLN* 3.8 24.7 - - - +
188A PRO* 3.3 24.4 - - - +
253A ILE* 4.5 19.1 - - + -
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Residues in contact with ILE 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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50A ASP* 3.2 20.8 + - + +
51A ASN* 3.5 18.2 - - - +
52A ARG 3.1 0.8 - - - -
53A THR* 1.3 75.3 - - - +
55A LEU* 1.3 63.2 + - - +
57A THR* 2.9 24.6 + - - -
58A TRP* 3.3 8.2 + - + +
253A ILE* 3.5 39.7 - - + +
254A LEU* 4.0 20.6 - - + +
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Residues in contact with LEU 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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41A TRP* 4.6 3.6 - - + -
51A ASN 2.9 17.7 + - - +
52A ARG 3.6 3.8 - - - +
54A ILE* 1.3 79.1 - - - +
56A LEU* 1.3 57.9 + - - +
58A TRP* 3.3 20.1 + - + +
59A MET* 3.0 32.3 + - - +
80A LEU* 3.7 39.0 - - + -
94A LEU* 3.7 47.3 - - + +
95A GLN* 4.0 10.5 - - - +
98A GLY* 4.1 15.0 - - - -
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Residues in contact with LEU 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 ARG* 2.7 65.5 + - + +
53A THR 4.0 4.5 - - - +
55A LEU* 1.3 74.3 - - - +
57A THR* 1.3 56.1 + - - +
59A MET* 4.0 12.1 - - - -
60A HIS* 3.0 30.5 + - - +
73A PHE* 3.4 6.0 - - + -
77A VAL* 3.7 27.4 - - + -
80A LEU* 3.9 22.9 - - + -
185A LEU 3.7 11.7 - - - +
186A ILE* 3.5 24.9 - - + +
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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
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53A THR 2.9 18.8 + - - -
54A ILE* 2.9 11.6 + - - -
56A LEU* 1.3 76.3 - - - +
58A TRP* 1.3 57.6 + - - +
60A HIS* 3.9 2.3 - - - +
61A LEU* 3.1 25.6 + - - +
186A ILE* 3.7 19.2 - - - +
249A TYR* 4.1 13.6 + - + -
250A ASP 4.4 9.1 + - - +
251A LEU* 3.9 26.9 - - + +
253A ILE* 4.3 14.4 - - + +
254A LEU* 4.1 16.6 - - + +
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Residues in contact with TRP 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 ILE 3.3 3.6 + - - +
55A LEU* 3.3 24.2 + - + +
56A LEU 3.2 0.4 - - - -
57A THR* 1.3 78.7 - - - +
59A MET* 1.3 64.8 + - + +
61A LEU* 3.2 17.9 + - + +
62A LEU* 2.9 61.5 + - + +
95A GLN* 3.5 52.5 - - + +
98A GLY 4.8 1.1 - - - -
99A ALA* 4.2 20.9 - - + -
119A LEU* 4.9 2.9 - - + -
122A LEU* 3.6 34.7 - - + +
254A LEU* 4.0 21.7 - - + +
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Residues in contact with MET 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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55A LEU* 3.0 36.5 + - + +
56A LEU* 3.4 17.0 + - + +
58A TRP* 1.3 87.3 - - + +
60A HIS* 1.3 63.8 + - - +
62A LEU* 3.0 10.8 + - - +
63A CYS* 2.9 27.5 + - - -
73A PHE* 3.6 14.6 - - + -
76A SER* 3.4 44.2 - - - +
77A VAL* 4.3 1.8 - - - +
80A LEU* 4.4 4.3 - - + -
98A GLY* 3.7 17.9 - - - +
101A CYS* 4.1 4.5 - - + -
102A VAL* 3.5 23.3 - - + -
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Residues in contact with HIS 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 LEU 3.0 18.0 + - - +
57A THR 3.9 2.9 - - - +
59A MET* 1.3 75.2 - - - +
61A LEU* 1.3 59.4 + - + +
63A CYS* 3.5 1.7 + - - +
64A GLU* 3.0 50.6 + - + +
73A PHE* 3.0 20.7 - - + -
179A THR* 4.5 3.9 - - + +
182A CYS* 3.6 29.4 + - + +
183A LYS* 3.4 42.4 + - + +
186A ILE* 3.6 16.2 - - + +
249A TYR* 4.5 16.2 - + - -
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Residues in contact with LEU 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 3.1 16.7 + - - +
58A TRP* 3.4 15.3 - - + +
59A MET 3.1 0.4 - - - -
60A HIS* 1.3 85.9 - - + +
62A LEU* 1.3 58.3 + - + +
64A GLU* 4.1 10.3 - - - +
65A SER* 2.7 47.1 + - - +
249A TYR* 4.8 4.7 - - - +
251A LEU* 4.5 24.5 - - + -
254A LEU* 4.1 22.9 - - + -
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Residues in contact with LEU 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 TRP* 2.9 61.9 + - + +
59A MET* 3.3 10.8 - - - +
61A LEU* 1.3 81.1 - - + +
63A CYS* 1.3 64.7 + - - +
65A SER* 4.7 1.3 - - - -
66A PHE* 3.1 39.2 + - + -
102A VAL* 4.9 7.2 - - + -
114A MET* 3.5 18.5 - - + +
119A LEU* 4.0 17.9 - - + -
122A LEU* 3.6 27.6 - - + -
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Residues in contact with CYS 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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59A MET 2.9 19.5 + - - +
60A HIS 4.1 3.1 - - - +
62A LEU* 1.3 74.9 - - - +
64A GLU* 1.3 63.3 + - - +
67A GLU* 3.3 1.7 + - - -
68A LEU* 3.1 45.8 + - + +
69A ASP 6.0 0.2 - - - +
72A VAL* 3.8 25.4 - - + -
73A PHE* 4.0 31.4 - - + +
76A SER* 4.7 0.9 - - - -
102A VAL* 3.9 19.5 - - - -
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Residues in contact with GLU 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 HIS* 3.0 41.3 + - + +
61A LEU* 4.1 12.6 - - - +
63A CYS* 1.3 74.4 - - - +
65A SER* 1.3 72.5 + - - +
67A GLU* 3.0 19.3 + - - +
179A THR* 5.2 8.0 - - - +
183A LYS* 4.8 9.4 - - - -
249A TYR* 5.5 3.2 + - - -
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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 LEU* 2.7 35.9 + - - +
62A LEU* 3.9 4.9 - - - -
64A GLU* 1.3 79.8 + - - +
66A PHE* 1.3 68.6 + - - +
67A GLU* 3.2 13.2 + - - +
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Residues in contact with PHE 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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62A LEU* 3.1 35.2 + - + +
65A SER* 1.3 82.8 - - - +
67A GLU* 1.3 71.8 + - - +
68A LEU* 3.2 18.6 + - + +
114A MET* 3.0 41.1 - - + -
118A LYS* 4.4 28.9 - - + -
122A LEU* 4.2 16.4 - - + -
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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