Contacts of the helix formed by residues 74 - 87 (chain A) in PDB entry 1YC9
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TRP 5.4 0.2 + - - -
72A TYR* 3.2 5.6 - - + +
73A GLN* 1.3 75.1 - - - +
75A ALA* 1.3 58.7 + - - +
76A GLN* 3.1 24.1 + - - +
77A LEU* 2.9 25.8 + - + +
78A ASN* 3.0 18.9 + - - +
193A TYR* 2.7 28.3 + - - -
279A PRO* 5.1 0.2 - - - +
280A HIS* 2.9 41.4 + - - +
281A ILE* 3.9 12.5 - - + +
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Residues in contact with ALA 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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73A GLN 4.0 3.0 + - - -
74A ASP* 1.3 72.6 + - - +
76A GLN* 1.3 52.9 + - - +
78A ASN* 3.4 14.7 - - + +
79A HIS* 2.8 36.2 + - - +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 3.1 14.1 + - - +
75A ALA* 1.3 70.6 - - - +
77A LEU* 1.3 63.8 + - - +
79A HIS* 3.3 5.6 + - - +
80A LEU* 3.0 29.8 + - + +
193A TYR* 2.9 26.6 + - + +
272A ARG* 5.1 6.5 + - - +
275A SER 3.7 5.7 + - - -
276A ILE* 3.3 19.4 - - - +
277A GLU* 2.8 53.6 - - - +
278A GLU 4.1 3.5 - - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 4.2 13.5 - - + +
72A TYR* 4.1 22.2 - - + -
74A ASP* 2.9 18.0 + - + +
76A GLN* 1.3 73.5 - - - +
78A ASN* 1.3 64.7 + - - +
80A LEU* 3.2 4.1 + - + +
81A ILE* 3.0 44.4 + - + +
189A ILE* 4.3 5.8 - - + -
190A ALA* 4.2 11.2 - - + -
193A TYR* 3.8 44.5 + - + -
281A ILE* 4.1 20.9 - - + -
465A PHE* 4.4 5.6 - - + -
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Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.2 28.0 - - - +
70A GLN* 3.6 34.7 + - - +
73A GLN* 5.5 1.2 - - - +
74A ASP 3.0 17.3 + - - +
75A ALA* 3.4 17.4 - - - +
77A LEU* 1.3 75.9 - - - +
79A HIS* 1.3 57.2 + - - +
81A ILE* 3.5 1.4 + - - +
82A GLU* 2.9 48.1 + - - +
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.8 20.4 + - - +
76A GLN* 3.7 6.5 - - - +
78A ASN* 1.3 70.4 - - - +
80A LEU* 1.3 60.9 + - - +
82A GLU* 3.8 11.2 - - + +
83A GLU* 2.4 78.5 + - + +
272A ARG* 4.1 6.2 + - - +
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Residues in contact with LEU 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 GLN* 3.0 25.3 + - + +
77A LEU* 3.2 7.2 + - - +
79A HIS* 1.3 75.5 - - - +
81A ILE* 1.3 64.2 + - - +
83A GLU* 3.5 4.2 + - - +
84A ALA* 3.2 17.2 + - - +
189A ILE* 4.1 13.2 - - + -
193A TYR* 3.8 33.0 - - + -
262A LEU* 4.5 18.6 - - + +
266A VAL* 3.3 31.7 - - + +
272A ARG* 3.3 33.7 - - + +
276A ILE* 4.5 14.4 - - + -
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Residues in contact with ILE 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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68A TRP* 4.8 0.2 - - + -
69A TRP* 3.6 68.2 - - + -
77A LEU* 3.0 27.4 + - + +
78A ASN 4.1 2.2 - - - +
80A LEU* 1.3 74.2 - - - +
82A GLU* 1.3 63.7 + - - +
84A ALA* 3.1 3.6 + - - +
85A LEU* 2.9 33.0 + - + +
186A SER* 3.8 25.8 - - - +
189A ILE* 3.6 27.8 - - + -
190A ALA* 4.6 4.3 - - + +
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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
----------------------------------------------------------
69A TRP* 3.6 24.4 + - + +
70A GLN* 3.7 16.1 + - - -
78A ASN* 2.9 36.5 + - - +
79A HIS* 3.8 12.1 - - + +
81A ILE* 1.3 76.0 - - - +
83A GLU* 1.3 61.2 + - - +
85A LEU* 3.3 6.3 + - - +
86A GLN* 3.1 28.3 + - - +
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Residues in contact with GLU 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 HIS* 2.4 60.4 + - + +
80A LEU* 3.6 6.3 - - - +
82A GLU* 1.3 72.1 - - - +
84A ALA* 1.3 63.3 + - - +
86A GLN* 3.2 9.2 + - - +
87A HIS 3.1 27.3 + - - +
266A VAL* 4.2 5.1 - - + +
268A GLN* 2.7 36.6 + - - +
272A ARG* 2.8 35.3 + - - -
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Residues in contact with ALA 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 LEU 3.2 4.2 + - - +
81A ILE 3.1 5.2 + - - +
83A GLU* 1.3 79.0 - - - +
85A LEU* 1.3 62.2 + - - +
86A GLN 3.5 0.7 + - - -
88A SER* 2.7 33.6 + - - +
91A LEU* 3.6 7.6 - - - +
185A ILE* 3.9 12.5 - - + +
189A ILE* 3.4 34.3 - - + -
265A LEU 4.2 1.8 - - - +
266A VAL* 3.9 15.9 - - - +
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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
----------------------------------------------------------
69A TRP* 3.6 33.4 - - + -
81A ILE* 2.9 27.0 + - + +
82A GLU* 4.0 6.1 - - - +
84A ALA* 1.3 74.0 - - - +
86A GLN* 1.3 58.1 + - - +
91A LEU* 3.2 26.2 - - + +
182A ARG* 3.8 41.7 - - + +
185A ILE* 3.8 34.3 - - + -
186A SER* 4.8 2.2 - - - +
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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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82A GLU* 3.1 19.3 + - - +
83A GLU* 3.2 8.2 + - - +
85A LEU* 1.3 78.7 - - - +
87A HIS* 1.3 65.9 + - + +
91A LEU* 3.2 11.3 - - - +
95A MET* 5.4 1.9 - - - +
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Residues in contact with HIS 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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83A GLU 3.1 14.2 + - - +
84A ALA 3.9 0.2 - - - -
86A GLN* 1.3 85.6 - - + +
88A SER* 1.3 65.4 + - - +
89A PRO* 5.8 1.1 - - + -
91A LEU* 3.7 4.2 - - - +
92A CYS* 4.0 24.1 - - - -
95A MET* 5.6 2.0 - - + -
266A VAL 4.1 5.9 - - - +
267A GLY 5.7 0.2 - - - +
268A GLN* 5.5 1.2 + - - -
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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