Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 1YV5
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 4.9 6.5 - - + -
31A PHE* 3.9 17.7 - + + -
32A VAL* 3.3 31.6 - - + +
67A ALA 3.5 20.4 - - - -
68A ILE* 3.5 15.5 - - + +
69A GLY* 2.9 23.6 + - - -
70A GLY* 3.3 21.7 - - - -
71A LYS* 1.3 90.0 - - - +
73A ASN* 1.3 64.9 + - - +
74A ARG 3.3 3.3 + - - -
75A GLY 3.4 1.2 + - - -
76A LEU* 3.0 27.0 + - + +
104A TRP* 3.7 20.9 - + - -
107A GLU* 3.6 26.8 + - - -
1001A PO4 4.3 4.0 + - - -
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Residues in contact with ASN 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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71A LYS* 3.2 41.2 - - + +
72A TYR* 1.3 78.4 - - - +
74A ARG* 1.3 60.9 + - + +
76A LEU* 3.5 7.6 + - - +
77A THR* 2.6 40.4 + - - +
107A GLU* 4.2 0.4 + - - -
253A PHE* 5.9 4.2 - - - -
361A LYS* 3.7 47.2 + - + +
362A ILE* 5.6 4.4 - - + +
1001A PO4 5.5 0.6 + - - -
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Residues in contact with ARG 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 TYR 3.3 0.6 - - - -
73A ASN* 1.3 85.2 - - + +
75A GLY* 1.3 61.3 + - - +
77A THR* 3.5 7.8 - - - -
78A VAL* 3.6 2.3 + - - +
106A VAL* 3.7 18.0 - - + +
107A GLU* 3.6 9.0 + - - +
110A GLN* 2.9 46.4 - - - +
215A THR* 5.4 1.4 - - - +
218A TYR* 3.9 19.1 + - - -
219A SER* 3.6 44.7 - - - +
220A PHE* 6.5 0.4 - - + -
223A PRO* 3.4 24.0 - - + +
253A PHE* 3.3 36.0 - - - -
1001A PO4 3.4 18.0 + - - -
1002A PO4 3.6 9.1 + - - -
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Residues in contact with GLY 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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31A PHE* 3.6 18.3 - - - -
72A TYR 3.4 0.4 + - - -
74A ARG* 1.3 75.6 - - - +
76A LEU* 1.3 62.2 + - - +
78A VAL* 3.3 11.4 + - - +
79A VAL* 3.6 3.8 + - - +
103A GLY* 3.2 40.7 - - - -
106A VAL* 4.5 0.9 - - - +
107A GLU* 3.1 15.3 + - - -
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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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27A GLU* 3.6 28.7 - - + +
28A LYS* 3.7 29.6 - - + +
31A PHE* 3.5 32.5 - - + -
71A LYS 4.4 3.6 - - - +
72A TYR* 3.0 29.1 + - + +
73A ASN* 3.9 8.3 - - - +
75A GLY* 1.3 73.2 - - - +
77A THR* 1.3 61.0 + - - +
79A VAL* 3.0 7.5 + - + +
80A VAL* 2.8 40.4 + - + +
100A TRP* 4.7 5.8 - - + -
361A LYS* 6.4 2.0 - - - -
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Residues in contact with THR 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 ASN* 2.6 24.4 + - - +
74A ARG* 3.5 10.3 - - - -
75A GLY 3.3 0.2 - - - -
76A LEU* 1.3 76.5 - - - +
78A VAL* 1.3 61.4 + - - +
80A VAL* 4.2 5.6 - - - +
81A ALA* 3.0 23.6 + - - +
220A PHE* 5.4 0.7 - - - +
223A PRO* 4.0 13.0 - - + -
224A ILE* 3.5 33.2 - - + -
358A LEU* 4.2 26.3 - - + +
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Residues in contact with VAL 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 ARG 3.6 2.9 + - - +
75A GLY 3.3 7.5 + - - +
76A LEU 3.2 0.8 - - - -
77A THR* 1.3 76.7 - - - +
79A VAL* 1.3 57.2 + - - +
82A PHE* 3.0 27.8 + - + +
99A ALA* 3.8 19.5 - - + +
102A VAL* 3.9 16.6 - - + +
103A GLY* 3.8 14.4 - - - +
106A VAL* 3.8 19.5 - - + -
223A PRO* 3.4 40.8 - - + +
226A ALA* 4.6 0.7 - - + -
227A ALA* 3.7 12.4 - - + +
230A MET* 4.7 7.0 - - - -
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Residues in contact with VAL 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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31A PHE* 4.2 4.7 - - + -
75A GLY 3.9 11.2 - - - +
76A LEU* 3.0 11.9 + - + +
78A VAL* 1.3 75.4 - - - +
80A VAL* 1.3 69.8 + - + +
82A PHE* 3.2 6.6 + - + +
83A ARG* 3.1 41.2 + - + +
96A LEU* 5.9 3.6 - - + -
99A ALA* 3.7 26.9 - - + +
100A TRP* 3.6 53.4 - - + -
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Residues in contact with VAL 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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27A GLU* 4.0 30.5 - - + +
76A LEU* 2.8 31.8 + - + +
77A THR* 4.2 5.2 - - - +
79A VAL* 1.3 75.7 - - + +
81A ALA* 1.3 63.2 + - - +
83A ARG* 3.3 7.9 + - - +
84A GLU* 3.2 42.5 + - - +
354A VAL* 6.1 1.6 - - - +
357A GLY* 6.5 1.6 - - - -
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Residues in contact with ALA 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 THR* 3.0 20.2 + - + +
80A VAL* 1.3 74.5 - - - +
82A PHE* 1.3 60.2 + - - +
84A GLU* 3.2 6.7 + - - +
85A LEU* 2.9 42.7 + - + +
224A ILE* 3.9 22.9 - - + -
227A ALA* 3.7 17.7 - - + -
354A VAL* 4.5 10.3 - - + -
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Residues in contact with PHE 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 VAL* 3.0 21.2 + - + +
79A VAL 3.2 5.6 + - - +
81A ALA* 1.3 78.3 - - - +
83A ARG* 1.3 62.5 + - + +
85A LEU* 4.9 0.9 - - - -
86A VAL* 3.0 69.0 + - + +
90A LYS 5.3 0.2 - - - -
91A GLN* 4.3 11.4 - - + -
95A SER* 3.7 39.9 - - - -
96A LEU* 4.3 17.5 - - + -
99A ALA* 3.6 21.8 - - + -
227A ALA* 3.8 9.6 - - + +
230A MET* 4.0 39.5 - - + -
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Residues in contact with ARG 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 VAL* 3.1 27.3 + - + +
80A VAL* 3.3 8.7 + - - +
82A PHE* 1.3 81.7 - - + +
84A GLU* 1.3 61.7 + - + +
86A VAL 3.7 2.6 - - - +
88A PRO* 5.6 1.6 - - - +
91A GLN* 2.9 47.0 + - - +
96A LEU* 4.0 29.5 - - + +
100A TRP* 5.5 6.3 - - - -
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Residues in contact with GLU 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 VAL* 3.2 33.2 + - + +
81A ALA* 3.8 4.4 - - - +
82A PHE 3.2 0.8 - - - -
83A ARG* 1.3 81.5 - - + +
85A LEU* 1.3 61.1 + - - +
86A VAL 4.8 1.2 - - - +
351A PRO* 4.0 17.9 - - + +
353A ALA* 4.3 17.1 - - - +
354A VAL* 2.9 44.6 + - + +
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Residues in contact with LEU 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 ALA* 2.9 31.6 + - + +
82A PHE* 4.3 1.1 - - - +
84A GLU* 1.3 79.5 - - - +
86A VAL* 1.3 61.1 + - + +
87A GLU 4.0 1.0 + - - -
224A ILE* 4.8 3.4 - - + +
227A ALA* 4.2 4.9 - - + -
228A MET* 4.0 37.2 - - + +
231A ALA* 3.9 19.7 - - + +
233A ILE* 4.2 9.3 - - + +
350A LEU* 3.9 22.2 - - + -
351A PRO* 3.7 29.2 - - + -
354A VAL* 4.2 11.7 - - + -
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Residues in contact with VAL 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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82A PHE* 3.0 49.6 + - + +
83A ARG 3.7 3.5 - - - +
84A GLU 4.8 1.0 - - - +
85A LEU* 1.3 78.1 - - - +
87A GLU* 1.3 73.5 + - - +
88A PRO* 3.3 3.5 - - - +
90A LYS* 3.8 19.7 - - + +
91A GLN* 2.9 36.0 + - + -
230A MET 4.8 0.2 - - - +
231A ALA* 3.5 27.4 - - + -
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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