Contacts of the helix formed by residues 69 - 85 (chain A) in PDB entry 1W7L
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 TYR 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.6 34.4 - - + +
64A THR* 3.5 24.9 - - + +
68A GLY* 1.3 68.9 - - - -
70A PRO* 1.3 62.9 - - + +
71A PRO* 3.5 36.2 - - + +
72A LEU* 2.7 34.4 + - + +
73A THR* 3.1 9.0 + - - +
282A THR* 4.2 5.8 - - + -
285A GLN* 2.7 38.2 + - + +
286A ALA* 3.5 38.6 - - + +
289A ALA* 4.7 2.2 - - + -
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Residues in contact with PRO 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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64A THR* 3.7 11.7 - - - +
65A LYS* 3.9 21.5 - - + -
68A GLY 3.1 7.4 - - - +
69A TYR* 1.3 84.9 - - + +
71A PRO* 1.3 67.7 - - + +
73A THR* 3.1 11.4 + - - +
74A LYS* 2.9 30.9 + - - +
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Residues in contact with PRO 71 (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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69A TYR* 3.5 39.5 - - + +
70A PRO* 1.3 97.3 - - + +
72A LEU* 1.3 59.8 + - - +
74A LYS* 3.6 11.8 - - + +
75A ILE* 3.3 24.3 + - - +
289A ALA* 3.8 9.0 - - + +
293A GLU* 4.4 10.2 - - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.7 23.6 + - + +
71A PRO* 1.3 72.3 - - - +
73A THR* 1.3 59.2 + - - +
74A LYS 3.2 0.4 + - - -
75A ILE* 3.4 5.4 - - + +
76A LEU* 2.9 55.0 + - + +
96A VAL* 3.8 20.6 - - + -
256A VAL* 4.1 11.2 - - + -
258A TRP* 5.8 0.7 - - + -
285A GLN* 3.7 46.0 - - + +
288A VAL* 3.7 23.1 - - + -
289A ALA* 3.7 18.0 - - + +
292A PHE* 4.6 0.7 - - + -
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Residues in contact with THR 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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67A PHE 3.9 8.1 - - - +
68A GLY* 3.8 30.9 + - - -
69A TYR 3.1 0.8 + - - -
70A PRO* 3.1 19.4 + - - +
72A LEU* 1.3 76.3 - - - +
74A LYS* 1.3 56.3 + - - +
76A LEU* 3.7 6.3 - - - +
77A ALA* 2.9 33.1 + - - +
90A PRO* 3.8 25.1 - - - +
94A VAL* 3.9 24.5 - - + +
96A VAL* 3.9 6.5 - - + -
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Residues in contact with LYS 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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70A PRO 2.9 17.9 + - - +
71A PRO* 3.6 11.9 - - + +
73A THR* 1.3 78.0 + - - +
75A ILE* 1.3 62.8 + - - +
77A ALA* 3.3 2.1 + - - +
78A SER* 3.1 26.3 + - - -
90A PRO* 4.3 14.1 - - + +
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Residues in contact with ILE 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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71A PRO 3.3 13.1 + - - +
72A LEU* 3.4 16.6 - - + +
74A LYS* 1.3 75.5 - - - +
76A LEU* 1.3 61.0 + - - +
78A SER* 4.3 4.9 - - - +
79A PHE* 2.8 38.4 + - + +
289A ALA* 3.9 25.1 - - + +
292A PHE* 3.8 26.0 - - + -
293A GLU* 4.0 24.2 - - + +
296A GLN* 3.3 42.8 - - + +
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Residues in contact with LEU 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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72A LEU* 2.9 39.3 + - + +
73A THR 3.7 4.0 - - - +
75A ILE* 1.3 77.2 - - - +
77A ALA* 1.3 58.6 + - - +
80A PHE* 2.9 64.7 + - + +
94A VAL* 3.7 29.4 - - + -
96A VAL* 4.3 5.6 - - + -
258A TRP* 3.8 33.7 - - + -
260A LEU* 4.7 4.0 - - + -
292A PHE* 3.9 24.7 - - + -
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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 THR 2.9 18.6 + - - +
74A LYS 3.3 3.8 + - - +
76A LEU* 1.3 76.0 - - - +
78A SER* 1.3 57.4 + - - +
81A GLY* 2.9 27.2 + - - -
88A ILE* 3.2 50.5 + - + +
90A PRO* 3.8 18.6 - - + -
94A VAL* 4.2 1.5 - - + +
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Residues in contact with SER 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 LYS* 3.1 18.5 + - - -
75A ILE* 4.1 6.8 - - - +
77A ALA* 1.3 75.4 - - - +
79A PHE* 1.3 63.4 + - - +
81A GLY* 3.9 0.5 - - - -
82A GLU* 3.2 22.2 + - - +
296A GLN* 2.8 24.3 + - - -
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Residues in contact with PHE 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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75A ILE* 2.8 28.3 + - + +
78A SER* 1.3 73.8 + - - +
80A PHE* 1.3 66.6 + + + +
82A GLU* 3.3 10.7 + - + +
83A LEU* 3.2 36.2 + - + +
218A TRP* 3.8 37.7 - + - -
292A PHE* 3.8 26.0 - + + -
296A GLN* 3.6 44.6 - - + +
299A PHE* 3.9 32.1 - + - -
306A PHE* 3.9 15.7 - + - -
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Residues in contact with PHE 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 LEU* 2.9 49.6 + - + +
79A PHE* 1.3 81.6 - + - +
81A GLY* 1.3 59.3 + - - +
83A LEU* 3.6 23.9 - - + -
84A LEU* 2.9 40.5 + - + +
88A ILE* 4.0 3.4 - - + -
217A GLN* 3.5 28.0 - - - -
218A TRP* 4.5 7.4 - + - -
241A THR* 6.5 0.4 - - + -
258A TRP* 3.8 26.2 - + - -
260A LEU* 3.6 30.3 - - + -
292A PHE* 3.9 21.5 - + - -
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Residues in contact with GLY 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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77A ALA 2.9 24.7 + - - -
78A SER 3.9 0.9 - - - -
79A PHE 3.3 0.2 - - - -
80A PHE* 1.3 77.8 - - - +
82A GLU* 1.3 54.7 + - - +
85A GLY* 3.1 8.7 + - - -
86A GLN* 2.9 45.5 + - - +
88A ILE* 3.6 9.6 - - - +
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Residues in contact with GLU 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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78A SER 3.2 13.6 + - - +
79A PHE* 3.5 13.2 - - + +
80A PHE 3.2 0.2 - - - -
81A GLY* 1.3 74.2 - - - +
83A LEU* 1.3 68.2 + - + +
85A GLY* 3.4 10.9 + - - -
296A GLN* 6.0 0.9 - - - +
299A PHE* 5.8 7.0 - - + -
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Residues in contact with LEU 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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79A PHE* 3.2 25.0 + - + +
80A PHE* 3.3 34.5 + - + +
82A GLU* 1.3 80.7 - - + +
84A LEU* 1.3 65.2 + - + +
85A GLY 3.8 0.2 + - - -
217A GLN* 3.9 10.5 - - - +
218A TRP* 3.7 29.6 - - + -
228A SER* 5.6 0.2 + - - -
231A SER* 5.1 2.3 - - - -
299A PHE* 3.6 35.2 - - + -
300A ARG* 5.9 0.9 - - - +
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Residues in contact with LEU 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 PHE* 2.9 25.0 + - + +
83A LEU* 1.3 82.8 - - + +
85A GLY* 1.3 63.6 + - - +
86A GLN* 4.1 11.6 - - + +
88A ILE* 4.1 10.5 - - + -
214A GLU* 5.2 0.7 - - - +
217A GLN* 6.2 0.9 - - - +
228A SER* 3.3 38.1 - - - +
230A ALA* 4.6 11.7 - - + -
231A SER* 3.1 34.0 - - - +
236A TRP* 4.0 29.8 - - + -
241A THR* 4.9 7.9 - - + +
260A LEU* 4.4 14.1 - - + -
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Residues in contact with GLY 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 GLY 3.1 7.2 + - - -
82A GLU* 3.4 9.9 + - - -
83A LEU 3.4 0.6 + - - -
84A LEU* 1.3 79.5 - - - +
86A GLN* 1.3 62.5 + - - +
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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