Contacts of the helix formed by residues 75 - 93 (chain A) in PDB entry 2Y01
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 LEU 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 1.3 70.8 - - - +
76A THR* 1.3 68.2 + - - +
77A ASN 3.1 1.6 - - - -
78A LEU* 2.9 31.7 + - + +
79A PHE* 3.6 13.6 + - + -
138A ASP* 5.1 2.0 - - - +
149A TYR* 4.2 16.6 - - + +
153A MET* 3.6 45.8 - - + +
154A THR* 3.8 4.3 - - - +
155A ARG* 3.7 48.5 - - + +
158A ALA* 4.3 6.7 - - + +
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.4 7.2 - - - -
75A LEU* 1.3 79.1 - - - +
77A ASN* 1.3 61.7 + - - +
79A PHE* 3.2 18.2 + - + +
80A ILE* 3.2 27.7 + - + +
135A ILE* 4.8 10.3 - - + -
138A ASP* 3.0 22.6 + - - +
139A ARG* 3.3 23.4 + - - +
149A TYR* 4.6 0.7 + - - -
292A LEU* 4.5 19.5 - - + -
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.8 15.9 - - + +
72A LEU* 3.0 53.4 + - - +
74A THR* 3.4 20.1 + - - +
75A LEU 3.1 1.0 - - - -
76A THR* 1.3 78.7 - - - +
78A LEU* 1.3 60.2 + - - +
80A ILE* 3.5 19.0 + - - +
81A THR* 2.9 30.5 + - - -
349A PHE* 4.2 12.8 - - - -
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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
----------------------------------------------------------
66A ILE* 5.9 2.0 - - + -
74A THR 3.5 10.2 + - - +
75A LEU* 2.9 23.8 + - + +
77A ASN* 1.3 78.9 - - - +
79A PHE* 1.3 60.0 + - + +
81A THR* 3.4 8.2 + - - +
82A SER 3.2 16.3 + - - -
155A ARG* 4.1 32.5 - - + +
158A ALA* 4.0 22.7 - - + -
159A LYS* 5.4 2.9 - - + +
162A ILE* 3.4 22.1 - - + +
402A Y01 3.4 56.2 - - + +
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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 LEU* 3.8 17.0 - - + -
76A THR* 3.2 13.4 + - - +
78A LEU* 1.3 76.2 - - - +
80A ILE* 1.3 59.2 + - - +
82A SER* 3.1 8.8 + - - -
83A LEU* 3.0 24.1 + - - +
131A THR* 3.5 14.4 - - + +
134A VAL* 3.7 28.7 - - + -
135A ILE* 3.5 26.5 - - + -
138A ASP* 3.8 33.4 - - + -
153A MET* 3.7 18.6 - - + -
158A ALA* 4.0 24.2 - - + -
161A ILE* 3.9 16.2 - - + -
162A ILE* 3.8 15.0 - - + -
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Residues in contact with ILE 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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62A VAL* 4.2 4.0 - - + -
66A ILE* 4.1 16.2 - - + -
76A THR* 3.2 18.2 + - + +
77A ASN* 3.5 23.3 - - - +
79A PHE* 1.3 76.4 - - - +
81A THR* 1.3 56.4 + - - +
83A LEU* 3.2 10.2 + - + +
84A ALA* 2.8 26.5 + - - +
135A ILE* 4.2 13.0 - - + -
292A LEU* 4.1 25.6 - - + -
295A ILE* 5.9 1.3 - - + -
343A TYR* 3.3 46.8 + - + +
349A PHE* 5.0 2.9 - - + -
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Residues in contact with THR 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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63A ILE* 4.4 26.1 + - + -
66A ILE* 3.6 24.7 - - - +
77A ASN 2.9 20.9 + - - -
78A LEU* 3.5 14.7 - - - +
79A PHE 3.3 0.4 - - - -
80A ILE* 1.3 76.3 - - - +
82A SER* 1.3 57.5 + - - +
84A ALA* 3.3 7.9 + - - +
85A CYS* 3.0 31.9 + - - -
402A Y01 4.4 29.0 + - + +
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Residues in contact with SER 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 LEU 3.2 12.2 + - - -
79A PHE* 3.1 11.4 + - - -
81A THR* 1.3 74.5 - - - +
83A LEU* 1.3 63.6 + - - +
85A CYS* 3.2 6.9 + - - +
86A ALA* 3.1 17.8 + - - +
131A THR* 4.0 14.1 + - - +
162A ILE* 3.6 25.0 - - - +
165A VAL* 5.6 0.2 - - - +
166A TRP* 2.9 34.0 + - - -
402A Y01 4.2 10.3 - - - +
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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
----------------------------------------------------------
79A PHE 3.0 10.8 + - - +
80A ILE* 3.4 9.9 - - + +
82A SER* 1.3 76.5 - - - +
84A ALA* 1.3 62.7 + - - +
86A ALA* 3.1 9.5 + - - +
87A ASP* 3.0 29.0 + - - +
128A SER* 4.9 16.4 - - - +
131A THR* 4.3 11.3 - - + +
132A LEU* 3.5 32.3 - - + -
135A ILE* 4.2 13.7 - - + -
295A ILE* 4.4 3.8 - - + -
339A ASN* 3.8 25.4 - - - +
343A TYR* 4.5 7.2 - - - +
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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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59A ASN* 3.7 24.3 - - - +
62A VAL* 4.2 16.6 - - + -
63A ILE* 3.8 23.3 - - + +
80A ILE 2.8 13.3 + - - +
81A THR* 3.3 9.1 + - - +
83A LEU* 1.3 75.8 - - - +
85A CYS* 1.3 56.9 + - - +
87A ASP* 3.4 3.5 + - - +
88A LEU* 2.8 30.2 + - - +
343A TYR* 6.2 0.4 - - + -
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Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.2 15.7 - - - -
81A THR* 3.0 23.2 + - - -
82A SER 3.2 8.0 + - - +
84A ALA* 1.3 73.6 - - - +
86A ALA* 1.3 65.5 + - - +
88A LEU* 3.3 9.0 + - - +
89A VAL* 3.0 32.8 + - + +
166A TRP* 4.6 1.3 - - - -
402A Y01 3.8 41.5 - - + -
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Residues in contact with ALA 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 SER 3.1 11.6 + - - +
83A LEU* 3.3 11.7 - - - +
85A CYS* 1.3 78.0 - - - +
87A ASP* 1.3 60.6 + - - +
89A VAL 3.4 0.5 + - - -
90A VAL* 3.3 19.2 + - - +
124A CYS* 3.5 24.6 - - - +
127A ALA* 4.7 0.7 - - + -
128A SER* 3.6 26.2 - - - +
166A TRP* 3.8 23.9 - - + -
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Residues in contact with ASP 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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55A ILE* 3.4 7.1 - - - +
59A ASN* 3.4 26.8 - - - +
83A LEU* 3.0 23.4 + - - +
84A ALA 3.8 2.7 - - - +
85A CYS 3.2 0.2 - - - -
86A ALA* 1.3 74.0 - - - +
88A LEU* 1.3 65.0 + - - +
90A VAL* 3.1 5.7 + - - +
91A GLY 3.0 18.0 + - - -
128A SER* 4.4 10.4 + - - -
335A ASN* 4.6 8.4 + - - +
336A SER* 2.6 40.2 + - - +
339A ASN* 4.0 22.2 + - - +
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Residues in contact with LEU 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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55A ILE* 4.9 1.8 - - - -
56A VAL* 4.0 41.1 - - + +
59A ASN* 4.4 9.6 - - + +
60A VAL* 4.3 14.8 - - + +
63A ILE* 3.9 22.7 - - + -
84A ALA 2.8 17.5 + - - +
85A CYS* 3.3 9.4 + - - +
87A ASP* 1.3 75.6 - - - +
89A VAL* 1.3 58.6 + - + +
91A GLY* 3.2 1.7 + - - +
92A LEU* 2.9 46.2 + - + +
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Residues in contact with VAL 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 CYS* 3.0 24.4 + - + +
86A ALA* 3.8 6.7 - - - +
87A ASP 3.2 0.2 - - - -
88A LEU* 1.3 75.0 - - + +
90A VAL* 1.3 59.9 + - - +
92A LEU* 4.5 5.6 - - + +
93A LEU* 2.9 45.4 + - + -
94A VAL* 3.2 9.0 + - + +
120A LEU* 4.7 9.4 - - + -
123A LEU* 5.8 0.7 - - + -
124A CYS* 3.8 18.4 - - - -
166A TRP* 5.2 3.6 - - + -
402A Y01 4.6 33.0 - - + -
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Residues in contact with VAL 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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55A ILE* 4.5 1.6 - - + -
86A ALA 3.3 14.1 + - - +
87A ASP* 3.1 8.7 + - - +
89A VAL* 1.3 76.8 - - - +
91A GLY* 1.3 59.8 + - - +
94A VAL* 3.2 21.4 + - + -
95A VAL* 2.7 49.3 + - + +
121A ASP* 6.2 0.4 - - - +
124A CYS* 3.7 22.7 - - + -
303A TRP* 6.4 1.8 - - + -
333A TYR* 4.1 16.2 - - + +
336A SER* 3.4 27.4 - - - +
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Residues in contact with GLY 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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52A VAL* 3.6 16.9 - - - +
55A ILE* 3.4 31.6 - - - +
56A VAL* 3.9 10.8 - - - -
87A ASP 3.0 10.5 + - - -
88A LEU 3.2 2.9 + - - -
90A VAL* 1.3 76.5 - - - +
92A LEU* 1.3 55.3 + - - +
95A VAL* 4.7 1.6 - - - -
96A PRO* 3.1 21.1 - - - +
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Residues in contact with LEU 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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52A VAL* 6.1 1.1 - - + -
56A VAL* 4.1 24.0 - - + -
88A LEU* 2.9 39.2 + - + +
89A VAL* 4.4 4.0 - - + +
91A GLY* 1.3 76.7 - - - +
93A LEU* 1.3 75.4 + - + +
96A PRO* 3.3 14.6 - - - +
97A PHE* 5.6 0.2 - - - -
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Residues in contact with LEU 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 VAL* 2.9 27.8 + - + +
91A GLY 3.6 0.6 - - - -
92A LEU* 1.3 93.2 - - + +
94A VAL* 1.3 65.3 + - - +
95A VAL 3.5 0.9 - - - -
96A PRO* 3.8 1.3 - - - -
97A PHE* 2.9 49.4 + - + +
117A TRP* 3.9 1.9 - - - -
120A LEU* 4.0 30.1 - - + -
402A Y01 4.7 11.4 - - + -
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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
------------------------------------------------------------
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