Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 1YL5
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLY 3.2 10.9 + - - +
79A PHE* 1.3 78.3 - - - +
81A ALA* 1.3 59.4 + - - +
82A GLU* 3.6 17.7 + - + +
83A ARG* 2.9 32.8 + - + +
84A PHE* 2.9 27.8 + - - +
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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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80A THR* 1.3 73.4 - - - +
82A GLU* 1.3 62.5 + - + +
84A PHE* 3.7 12.1 - - + +
85A GLN* 3.0 28.9 + - - +
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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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80A THR* 3.1 15.4 + - - +
81A ALA* 1.3 80.9 - - + +
83A ARG* 1.3 62.7 + - - +
85A GLN* 4.0 3.9 + - - +
86A GLN* 3.5 20.3 + - - +
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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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55A PRO* 3.0 35.6 + - - +
56A ASP* 4.4 8.9 + - - +
58A VAL* 4.1 8.9 - - - +
59A MET* 3.4 38.9 - - - +
77A THR 4.6 0.4 + - - -
78A GLY 3.5 20.5 + - - +
79A PHE* 3.8 16.5 - - + -
80A THR* 2.9 42.2 + - + +
82A GLU* 1.3 75.9 - - - +
84A PHE* 1.3 64.3 + - - +
86A GLN* 3.3 6.2 - - - +
87A VAL* 3.2 25.1 + - - +
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Residues in contact with PHE 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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79A PHE* 3.4 46.4 - + + -
80A THR 2.9 16.8 + - - +
81A ALA* 3.7 12.8 - - + +
83A ARG* 1.3 76.5 - - - +
85A GLN* 1.3 63.4 + - - +
87A VAL* 3.0 17.1 + - - +
88A GLU* 3.1 17.2 + - - +
101A ILE* 3.7 24.5 - - + -
234A LEU* 3.9 8.7 - - + +
236A VAL* 3.4 43.1 - - + -
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Residues in contact with GLN 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 3.0 18.3 + - - +
82A GLU* 4.4 4.3 - - - +
83A ARG 3.4 0.4 - - - -
84A PHE* 1.3 75.1 - - - +
86A GLN* 1.3 53.4 + - - +
88A GLU* 3.1 19.4 + - - +
89A SER* 2.7 48.3 + - - +
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Residues in contact with GLN 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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59A MET* 3.7 10.8 - - + -
82A GLU 3.5 13.7 + - - +
83A ARG 3.3 11.4 + - - +
84A PHE 3.2 0.2 - - - -
85A GLN* 1.3 78.0 - - - +
87A VAL* 1.3 57.3 + - - +
89A SER* 3.3 14.8 + - - -
90A TRP* 2.9 74.8 + - + +
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Residues in contact with VAL 87 (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* 4.4 10.8 - - + -
62A LEU* 3.7 26.0 - - + -
66A ILE* 4.1 8.3 - - + -
79A PHE* 4.5 1.1 - - + -
83A ARG 3.2 14.8 + - - +
84A PHE* 3.0 9.2 + - - +
86A GLN* 1.3 76.9 - - - +
88A GLU* 1.3 56.7 + - - +
90A TRP* 3.3 13.6 + - + +
91A LEU* 2.9 50.1 + - + +
99A VAL* 4.1 18.2 - - + -
101A ILE* 4.5 8.3 - - + -
234A LEU* 4.1 15.3 - - + -
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Residues in contact with GLU 88 (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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84A PHE 3.1 7.9 + - - +
85A GLN* 3.1 23.9 + - - +
87A VAL* 1.3 71.3 - - - +
89A SER* 1.3 64.9 + - - +
91A LEU* 3.6 9.3 - - - +
92A VAL* 3.0 28.1 + - - +
233A GLY* 5.1 1.7 - - - -
234A LEU* 3.7 44.8 + - + +
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Residues in contact with SER 89 (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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85A GLN* 2.7 34.7 + - - +
86A GLN* 3.4 22.5 + - - -
88A GLU* 1.3 72.1 - - - +
90A TRP* 1.3 65.0 + - - +
92A VAL* 3.2 23.9 + - - +
93A ALA* 3.9 3.8 + - - +
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Residues in contact with TRP 90 (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* 3.3 50.5 - - + -
62A LEU* 4.2 6.1 - - + -
63A GLU* 3.5 56.2 + - + +
66A ILE* 3.4 35.5 - - + +
86A GLN* 2.9 51.0 + - + +
87A VAL* 3.3 11.0 + - + +
89A SER* 1.3 76.3 - - - +
91A LEU* 1.3 61.4 + - - +
93A ALA* 3.4 15.6 + - - +
94A LYS* 3.6 5.4 + - - +
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Residues in contact with LEU 91 (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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66A ILE* 3.7 28.9 - - + -
87A VAL* 2.9 38.6 + - + +
88A GLU* 3.6 10.1 - - - +
89A SER 3.2 0.2 - - - -
90A TRP* 1.3 75.2 - - - +
92A VAL* 1.3 66.8 + - - +
93A ALA 3.2 0.2 - - - -
94A LYS 2.9 24.0 - - - +
95A PRO* 3.5 4.0 - - - +
97A THR* 3.4 32.8 - - + +
99A VAL* 4.1 7.4 - - + -
233A GLY* 3.8 8.7 - - - -
234A LEU* 3.7 31.9 - - + +
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Residues in contact with VAL 92 (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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88A GLU 3.0 20.4 + - - +
89A SER* 3.2 12.9 + - - +
91A LEU* 1.3 78.0 - - - +
93A ALA* 1.3 65.6 + - + +
94A LYS 3.3 0.3 + - - -
95A PRO* 3.6 15.6 - - - +
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Residues in contact with ALA 93 (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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89A SER 3.9 3.0 + - - +
90A TRP* 3.4 10.2 + - - +
91A LEU 3.2 0.4 - - - -
92A VAL* 1.3 82.3 - - + +
94A LYS* 1.3 77.2 + - + +
95A PRO* 3.6 6.4 - - - +
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Residues in contact with LYS 94 (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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66A ILE* 2.9 39.0 - - + +
67A ASP* 2.8 40.0 + - - +
69A GLY* 5.1 3.1 - - - +
90A TRP 3.6 3.9 + - - +
91A LEU* 2.9 19.7 + - - +
93A ALA* 1.3 94.5 - - - +
95A PRO* 1.3 65.4 - - - +
97A THR* 3.5 21.8 + - - +
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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