Contacts of the helix formed by residues 58 - 72 (chain X) in PDB entry 1XW4
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 ASP 58 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57X LEU* 1.3 71.6 - - - +
59X PRO* 1.4 70.8 - - - +
60X ALA* 3.0 19.4 + - - +
61X LYS* 2.9 31.8 + - + +
62X VAL* 3.0 13.0 + - - +
100X HIS* 2.9 17.9 + - + +
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Residues in contact with PRO 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X LEU* 3.6 11.4 - - + +
58X ASP* 1.4 87.9 - - - +
60X ALA* 1.3 59.8 + - - +
62X VAL* 3.4 11.9 + - + +
63X GLN* 3.1 22.2 + - - +
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Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ASP* 3.0 11.8 + - - +
59X PRO* 1.3 77.7 - - - +
61X LYS* 1.3 61.0 + - - +
63X GLN* 3.4 6.9 + - - +
64X SER* 2.9 28.1 + - - -
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Residues in contact with LYS 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ASP* 2.9 26.1 + - + +
60X ALA* 1.3 76.2 - - - +
62X VAL* 1.3 64.0 + - - +
64X SER* 3.4 6.6 + - - -
65X LEU* 3.1 22.3 + - + +
100X HIS* 3.5 38.0 + - + -
998X ADP 2.3 62.5 + - + +
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Residues in contact with VAL 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X LEU* 4.0 24.7 - - + -
58X ASP 3.0 12.6 + - - +
59X PRO* 3.6 10.5 - - + +
61X LYS* 1.3 76.3 - - - +
63X GLN* 1.3 58.4 + - - +
65X LEU* 3.3 9.2 + - - +
66X VAL* 2.9 25.0 + - + +
100X HIS* 3.6 26.0 - - + -
103X ALA* 4.1 18.8 - - + -
104X ALA* 3.8 10.4 - - - +
107X GLN* 3.6 34.1 - - - +
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Residues in contact with GLN 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PRO 3.1 16.6 + - - +
60X ALA* 3.8 7.2 - - - +
61X LYS 3.3 0.2 - - - -
62X VAL* 1.3 74.2 - - - +
64X SER* 1.3 65.8 + - - +
66X VAL* 3.2 17.7 + - - +
67X ASP* 3.0 54.0 + - - +
70X ARG* 4.9 3.3 + - - -
107X GLN* 4.0 17.4 + - - -
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Residues in contact with SER 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X ALA 2.9 18.2 + - - -
61X LYS* 3.5 9.6 - - - -
63X GLN* 1.3 75.4 - - - +
65X LEU* 1.3 55.9 + - - +
67X ASP* 3.3 11.9 + - - +
68X THR* 2.9 31.2 + - - -
998X ADP 2.6 31.4 + - - -
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Residues in contact with LEU 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LYS* 3.1 17.1 + - + +
62X VAL 3.5 7.6 - - - +
64X SER* 1.3 76.1 - - - +
66X VAL* 1.3 59.4 + - - +
68X THR* 3.8 1.5 - - - -
69X ILE* 2.8 39.7 + - + +
76X VAL* 3.9 28.5 - - + -
100X HIS* 3.3 42.4 - - + -
101X ARG* 3.8 10.3 - - + +
104X ALA* 3.7 11.0 - - + -
998X ADP 3.6 45.3 - - + +
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Residues in contact with VAL 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X VAL* 2.9 22.1 + - + +
63X GLN* 3.2 22.1 + - - +
65X LEU* 1.3 76.4 - - - +
67X ASP* 1.3 62.3 + - - +
69X ILE* 3.4 2.1 + - - +
70X ARG* 3.1 39.0 + - - +
104X ALA* 3.7 28.7 - - + +
107X GLN* 4.1 22.4 - - + +
108X LEU* 3.8 30.9 - - + +
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Residues in contact with ASP 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X GLN* 3.0 38.6 + - - +
64X SER* 3.5 10.9 - - - +
66X VAL* 1.3 75.7 - - - +
68X THR* 1.3 64.0 + - - +
70X ARG* 3.5 16.8 + - - +
71X GLU* 3.1 32.6 + - + +
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Residues in contact with THR 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X SER 2.9 17.7 + - - -
65X LEU* 3.3 4.5 + - - -
67X ASP* 1.3 77.2 - - - +
69X ILE* 1.3 55.0 + - - +
71X GLU* 4.6 2.0 - - - +
72X ASP* 2.7 43.6 + - + +
75X SER* 3.2 26.5 - - - +
76X VAL* 3.6 9.4 - - + -
998X ADP 3.0 34.6 + - - +
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Residues in contact with ILE 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X LEU* 2.8 27.5 + - + +
66X VAL 3.8 3.1 - - - +
68X THR* 1.3 71.8 - - - +
70X ARG* 1.3 61.0 + - - +
73X PRO* 3.4 32.4 - - + +
76X VAL* 4.1 17.9 - - + -
101X ARG* 4.8 0.9 - - - +
104X ALA* 3.7 23.3 - - + -
105X TYR* 3.4 53.8 - - + +
108X LEU* 3.5 19.7 - - + -
110X ARG* 3.8 21.3 + - - +
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Residues in contact with ARG 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X GLN* 4.9 3.2 + - - -
66X VAL* 3.1 32.6 + - - +
67X ASP* 3.6 17.0 + - - +
69X ILE* 1.3 77.8 - - - +
71X GLU* 1.3 62.9 + - + +
73X PRO* 4.6 2.6 - - - +
108X LEU* 3.4 33.1 - - + +
110X ARG* 4.9 7.6 - - - +
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Residues in contact with GLU 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X ASP* 3.1 22.6 + - - +
68X THR* 4.5 1.3 - - - +
70X ARG* 1.3 79.6 - - + +
72X ASP* 1.3 65.0 + - + +
73X PRO* 3.9 3.4 - - - +
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Residues in contact with ASP 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X THR* 2.7 23.2 + - + +
71X GLU* 1.3 78.3 - - + +
73X PRO* 1.4 62.2 - - - +
74X ASP* 4.2 9.5 + - - +
75X SER* 2.5 58.3 + - - +
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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