Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 1W6J
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A HIS* 1.3 87.2 - - + +
73A ALA* 1.3 65.4 + - - +
74A PHE* 4.0 0.5 - - - +
75A GLU* 3.3 31.9 + - - +
76A GLY 3.0 18.9 + - - -
678A LEU* 3.4 13.5 - - - +
727A ALA 3.7 12.1 - - - +
728A LEU* 3.2 12.3 - - - +
730A GLY* 3.5 29.3 + - - -
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Residues in contact with ALA 73 (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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72A THR* 1.3 71.8 - - - +
74A PHE* 1.3 56.8 + - - +
77A ALA* 2.9 31.5 + - - +
674A VAL* 4.2 11.2 - - + -
678A LEU* 4.3 2.0 - - - +
716A LEU* 3.5 39.5 - - + +
719A PHE* 3.8 20.2 - - + -
720A SER* 4.0 2.0 - - - -
728A LEU* 2.8 17.0 + - - +
729A ALA 3.8 5.4 - - - +
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Residues in contact with PHE 74 (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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72A THR* 3.2 3.6 - - - +
73A ALA* 1.3 78.1 - - - +
75A GLU* 1.3 69.2 + - + +
77A ALA* 3.8 4.9 - - + +
78A LEU* 2.9 49.3 + - + +
81A MET* 6.5 0.7 - - + -
399A ALA 5.3 10.3 - - - -
404A ARG* 4.0 24.7 - - - -
720A SER* 4.1 7.8 - - - -
729A ALA 3.0 19.6 + - - +
730A GLY 4.1 11.0 - - - +
732A PRO* 3.4 30.1 - - + -
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Residues in contact with GLU 75 (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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68A PRO 5.8 0.2 - - - +
69A LYS 4.0 5.5 - - - +
70A ALA* 3.5 17.0 - - + -
71A HIS* 2.9 29.8 + - - +
72A THR* 3.3 22.6 + - - +
74A PHE* 1.3 85.7 - - + +
76A GLY* 1.3 61.0 + - - +
78A LEU* 3.8 5.3 - - + +
79A ASN* 2.9 36.8 + - - +
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Residues in contact with GLY 76 (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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70A ALA* 3.3 15.4 - - - +
72A THR 3.0 10.9 + - - -
73A ALA 3.8 0.4 - - - -
75A GLU* 1.3 77.3 - - - +
77A ALA* 1.3 56.4 + - - +
80A GLY 2.9 23.7 + - - -
678A LEU* 3.7 17.0 - - - -
681A GLN* 3.0 18.6 + - - -
687A TRP* 3.7 2.8 - - - -
716A LEU* 3.9 7.9 - - - -
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Residues in contact with ALA 77 (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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73A ALA 2.9 17.9 + - - +
74A PHE* 3.8 5.4 - - + +
76A GLY* 1.3 74.1 - - - +
78A LEU* 1.3 58.5 + - - +
80A GLY* 3.2 1.2 + - - -
81A MET* 2.9 36.3 + - + +
399A ALA* 4.0 24.0 - - + +
713A ILE* 4.2 11.5 - - - +
716A LEU* 3.9 17.9 - - + +
717A GLY* 4.1 7.6 - - - +
720A SER* 5.8 0.2 - - - +
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Residues in contact with LEU 78 (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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74A PHE* 2.9 36.1 + - + +
75A GLU* 3.8 7.2 - - + +
77A ALA* 1.3 76.4 - - - +
79A ASN* 1.3 60.7 + - - +
81A MET* 3.2 13.1 + - + +
82A THR* 2.9 44.0 + - - +
404A ARG* 3.8 49.1 - - - +
406A GLU* 4.4 1.8 - - - +
407A PHE* 4.0 13.7 - - + -
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Residues in contact with ASN 79 (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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67A LEU* 3.7 33.3 + - + +
68A PRO* 2.8 31.4 + - - +
69A LYS* 4.7 0.8 - - - +
70A ALA* 3.9 13.3 - - - +
75A GLU* 2.9 22.9 + - - +
78A LEU* 1.3 80.5 - - - +
80A GLY* 1.3 62.4 + - - +
82A THR* 3.4 3.3 + - - -
83A PHE 3.0 18.9 + - - -
681A GLN* 3.6 21.1 + - - +
682A LEU 5.8 0.4 + - - -
683A PRO 5.4 1.4 + - - -
685A GLY* 3.5 12.3 - - - -
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Residues in contact with GLY 80 (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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76A GLY 2.9 12.4 + - - -
77A ALA 3.6 3.4 - - - -
78A LEU 3.2 0.4 - - - -
79A ASN* 1.3 77.3 - - - +
81A MET* 1.3 55.8 + - - +
83A PHE* 3.5 2.9 + - - +
84A TYR* 2.9 30.1 + - - +
681A GLN* 3.4 0.4 - - - +
685A GLY 3.4 16.2 - - - +
687A TRP* 3.6 20.7 - - - -
709A ASN* 5.3 0.9 - - - +
713A ILE* 3.5 8.8 - - - +
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Residues in contact with MET 81 (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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74A PHE* 6.5 0.7 - - + -
77A ALA* 2.9 19.9 + - + +
78A LEU* 3.7 16.4 - - + +
80A GLY* 1.3 72.2 - - - +
82A THR* 1.3 61.2 + - - +
84A TYR* 4.4 2.0 - - - +
85A VAL* 2.8 36.8 + - + +
396A LEU* 3.5 32.8 - - + +
399A ALA* 3.6 40.2 - - + +
400A GLY 4.8 0.2 - - - -
401A GLY* 3.8 26.5 - - - -
404A ARG* 5.3 2.5 - - + -
407A PHE* 3.6 22.7 - - + -
713A ILE* 3.6 14.1 - - + -
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Residues in contact with THR 82 (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 PHE* 6.2 0.2 - - - -
65A LYS* 6.4 0.9 - - - -
67A LEU* 3.9 26.0 - - + -
78A LEU* 2.9 24.7 + - - +
79A ASN* 3.7 5.9 + - - -
81A MET* 1.3 77.9 - - - +
83A PHE* 1.3 63.2 + - - +
85A VAL* 4.4 1.4 - - - +
86A GLY* 3.8 9.9 + - - -
406A GLU* 5.2 1.0 + - - -
407A PHE* 3.7 20.1 - - + -
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Residues in contact with PHE 83 (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 TYR* 3.8 20.9 - + - -
60A THR* 5.4 0.7 - - - -
64A PHE* 3.8 33.9 - + + -
79A ASN 3.0 7.9 + - - +
80A GLY 3.8 2.0 - - - +
82A THR* 1.3 76.5 - - - +
84A TYR* 1.3 67.0 + - + +
86A GLY* 3.0 17.3 + - - -
87A LEU* 3.7 26.1 + - + +
684A ASN* 3.4 49.0 + - - +
685A GLY 3.7 13.2 - - - -
686A ASP* 3.2 44.9 - - + -
709A ASN* 3.9 10.5 - - - -
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Residues in contact with TYR 84 (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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80A GLY 2.9 21.5 + - - +
81A MET* 4.3 1.3 - - - +
83A PHE* 1.3 76.8 - - - +
85A VAL* 1.3 63.0 + - + +
87A LEU* 2.9 27.3 + - + +
94A TRP* 3.0 67.8 + + - +
388A ASP* 4.7 0.7 + - - +
392A ALA* 3.7 18.7 - - + +
396A LEU* 5.0 7.2 - - + -
706A SER* 2.7 37.0 + - - -
709A ASN* 3.4 38.6 - - + -
710A ILE* 3.5 15.4 - - + +
713A ILE* 4.1 17.0 - - + -
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Residues in contact with VAL 85 (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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81A MET* 2.8 31.6 + - + +
82A THR 4.4 2.5 - - - +
84A TYR* 1.3 72.0 - - - +
86A GLY* 1.3 60.7 - - - +
87A LEU 3.2 1.2 + - - -
88A GLN* 3.2 19.0 + - - +
94A TRP* 4.5 7.6 - - + -
396A LEU* 4.1 17.7 - - + -
406A GLU 5.2 3.1 - - - +
407A PHE* 3.7 31.4 - - + -
410A CYS* 3.9 35.0 - - + -
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Residues in contact with GLY 86 (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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51A LEU* 4.9 5.9 + - - +
64A PHE* 3.9 26.0 - - - -
82A THR 3.8 6.0 + - - -
83A PHE 3.0 11.8 + - - -
85A VAL* 1.3 78.3 - - - +
87A LEU* 1.3 61.6 + - - +
88A GLN 3.5 3.7 - - - +
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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