Contacts of the helix formed by residues 86 - 101 (chain A) in PDB entry 2Y4U
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 LYS 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LEU* 5.2 4.1 - - - +
81A PHE* 3.6 42.4 - - + +
82A LEU* 4.3 1.8 + - - -
84A MSE 2.6 48.3 + - + -
85A GLY* 1.3 70.6 - - - -
87A SER* 1.3 62.9 + - - +
88A LYS 3.7 1.1 - - - -
89A ALA* 4.4 8.1 - - + -
90A ALA* 3.7 18.2 + - - +
186A TRP* 4.8 3.4 - - - -
219A ASN* 5.8 6.8 - - - +
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Residues in contact with SER 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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85A GLY 3.7 4.0 + - - -
86A LYS* 1.3 70.3 - - - +
88A LYS* 1.3 74.5 + - - +
89A ALA 3.2 1.5 + - - -
90A ALA* 3.4 9.6 + - - +
91A LEU 3.6 7.3 + - - -
114A LEU* 3.9 9.0 - - - +
118A GLN* 3.8 21.1 + - - +
186A TRP* 3.1 43.6 + - - +
217A LEU* 3.5 25.4 + - - +
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 1.3 85.0 + - - +
89A ALA* 1.3 58.1 + - + +
90A ALA 3.1 0.9 + - - -
91A LEU* 3.4 2.3 + - - +
92A PRO* 2.9 27.7 - - - +
118A GLN* 5.1 4.3 - - - +
217A LEU 4.0 11.9 + - - +
218A LYS* 3.3 53.3 + - - +
219A ASN* 5.4 4.7 - - + +
220A ASP* 4.1 9.9 + - - +
221A ASN* 5.7 0.4 - - - +
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Residues in contact with ALA 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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81A PHE* 3.2 49.4 - - + -
86A LYS* 4.1 11.5 + - + -
87A SER 3.2 0.8 - - - -
88A LYS* 1.3 78.5 - - - +
90A ALA* 1.3 60.5 + - - +
92A PRO* 3.5 15.0 - - - +
93A ASP* 3.7 5.4 - - - +
219A ASN* 6.0 4.0 - - - +
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Residues in contact with ALA 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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78A ALA* 4.1 6.9 - - + +
81A PHE* 3.7 26.4 - - + -
82A LEU* 3.7 27.8 - - + -
86A LYS 3.7 7.9 + - - +
87A SER 3.4 1.7 + - - +
88A LYS 3.1 0.6 - - - -
89A ALA* 1.3 78.3 - - - +
91A LEU* 1.3 66.5 + - - +
93A ASP* 2.9 15.5 + - - +
94A LEU* 3.0 14.4 + - + +
114A LEU* 3.8 7.6 - - + -
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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
----------------------------------------------------------
87A SER 3.6 0.4 + - - -
88A LYS 3.4 5.9 + - - +
90A ALA* 1.3 76.0 - - - +
92A PRO* 1.3 79.2 - - + +
94A LEU* 2.9 15.2 + - - +
95A THR* 3.0 30.7 + - + +
111A ARG* 5.4 3.6 - - + -
114A LEU* 3.5 13.3 - - + +
115A LEU* 3.9 27.1 - - + -
118A GLN* 3.6 32.5 - - - +
120A LYS* 5.1 8.1 - - - +
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Residues in contact with PRO 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 LYS 2.9 26.5 - - - +
89A ALA* 3.5 14.8 - - - +
90A ALA 3.6 0.2 - - - -
91A LEU* 1.3 93.3 - - + +
93A ASP* 1.3 66.3 + - - +
95A THR* 3.3 8.7 + - - +
96A LYS* 3.1 24.1 + - - +
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Residues in contact with ASP 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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74A TYR* 3.7 17.0 - - - +
77A ARG* 2.6 59.5 + - - +
78A ALA* 3.7 15.9 - - + -
81A PHE* 3.6 4.5 - - - -
89A ALA 3.7 14.6 - - - +
90A ALA 2.9 10.5 + - - +
92A PRO* 1.3 79.7 - - - +
94A LEU* 1.3 63.8 + - - +
96A LYS* 3.9 3.7 - - - +
97A VAL* 3.3 25.5 + - - +
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Residues in contact with LEU 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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75A TYR* 4.6 19.5 - - + -
78A ALA* 4.0 19.5 - - + -
79A THR* 6.2 0.9 - - + -
82A LEU* 4.9 13.7 - - + -
90A ALA 3.0 8.5 + - - +
91A LEU 2.9 8.5 + - - +
93A ASP* 1.3 76.1 - - - +
95A THR* 1.3 64.7 + - - +
97A VAL* 3.1 8.8 + - + +
98A ILE* 3.1 24.6 + - - +
107A ALA* 4.4 7.1 - - + +
110A GLN* 3.9 24.5 - - + +
111A ARG* 3.7 37.0 - - + +
114A LEU* 3.9 23.8 - - + -
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Residues in contact with THR 95 (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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91A LEU* 3.0 29.8 + - + +
92A PRO* 3.3 11.6 + - - +
94A LEU* 1.3 72.8 - - - +
96A LYS* 1.3 61.8 + - - +
98A ILE* 3.3 4.3 + - - +
99A GLN* 2.9 38.8 + - - +
111A ARG* 3.3 46.2 - - + +
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Residues in contact with LYS 96 (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 PRO* 4.1 9.6 + - - +
69A ASP* 5.9 1.6 + - - +
74A TYR* 3.7 49.9 + - + -
92A PRO 3.1 13.5 + - - +
93A ASP* 3.9 5.8 - - - +
95A THR* 1.3 78.9 + - - +
97A VAL* 1.3 59.3 + - - +
99A GLN* 3.3 18.5 + - + +
100A LEU* 2.8 49.1 + - + +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.8 19.1 - - + +
74A TYR* 3.6 7.9 - - + -
75A TYR* 3.5 38.6 - - + +
93A ASP 3.3 16.6 + - - +
94A LEU* 3.1 11.6 + - + +
96A LYS* 1.3 73.8 - - - +
98A ILE* 1.3 68.6 + - - +
100A LEU* 3.1 5.4 + - - -
101A LYS* 2.8 25.3 + - + +
104A PHE* 4.2 15.9 - - + -
107A ALA* 3.7 24.7 - - + -
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Residues in contact with ILE 98 (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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94A LEU 3.1 18.4 + - - +
95A THR* 3.4 7.0 - - - +
97A VAL* 1.3 80.9 - - - +
99A GLN* 1.3 69.3 + - + +
101A LYS 4.5 4.0 - - - -
102A MSE 3.0 34.7 + - + +
104A PHE 5.2 2.9 - - - +
107A ALA* 4.0 8.3 - - + +
108A ARG* 3.4 68.2 - - + +
111A ARG* 3.3 44.4 - - - +
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Residues in contact with GLN 99 (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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95A THR* 2.9 29.8 + - - +
96A LYS* 3.6 19.4 + - + +
98A ILE* 1.3 78.0 - - + +
100A LEU* 1.3 64.9 + - + +
102A MSE 4.2 23.1 + - + +
111A ARG* 6.1 0.7 - - - +
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Residues in contact with LEU 100 (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 PRO 4.3 0.2 - - - +
69A ASP* 3.2 34.8 - - + +
70A ASN 3.6 16.2 - - - +
71A TYR* 3.9 17.7 - - + -
74A TYR* 4.3 1.3 - - + -
96A LYS* 2.8 53.5 + - + +
97A VAL 3.7 1.8 - - - +
99A GLN* 1.3 77.3 - - + +
101A LYS* 1.3 60.7 + - - +
102A MSE 3.7 1.9 + - - +
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Residues in contact with LYS 101 (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 TYR* 3.4 57.7 + - + -
97A VAL* 2.8 14.2 + - - +
98A ILE* 3.3 6.0 - - - +
100A LEU* 1.3 73.5 - - - +
102A MSE 1.4 53.2 + - - +
103A ASP* 2.8 33.9 + - + +
104A PHE* 2.9 40.8 + - + +
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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