Contacts of the helix formed by residues 81 - 100 (chain A) in PDB entry 4YYD
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 SER 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.5 13.6 - - - +
29A LEU* 5.2 0.2 - - - -
79A TYR* 3.4 6.2 - - - +
80A LYS* 1.4 81.4 - - - +
82A VAL* 1.3 63.6 - - - +
83A THR* 3.4 12.5 + - - -
84A GLU* 3.0 38.5 + - - +
85A PHE* 3.3 11.4 + - - +
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Residues in contact with VAL 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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25A ILE* 3.9 14.8 - - + +
28A LEU* 3.8 27.4 - - + -
29A LEU* 4.1 17.3 - - + -
32A PHE* 4.0 19.7 - - + -
81A SER* 1.3 71.2 - - - +
83A THR* 1.3 57.7 + - - +
85A PHE* 3.1 2.3 + - + +
86A LYS* 2.8 49.0 + - + +
121A MET 4.6 6.3 - - - +
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.2 11.3 + - - +
82A VAL* 1.3 78.0 - - - +
84A GLU* 1.3 64.8 + - + +
86A LYS* 3.4 10.0 + - - +
87A ALA* 3.0 23.5 + - + +
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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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78A GLU 3.9 3.5 - - - +
79A TYR* 3.7 20.5 - - + -
80A LYS* 2.8 47.4 + - - +
81A SER* 3.0 20.4 + - - +
83A THR* 1.3 79.6 - - + +
85A PHE* 1.3 63.4 + - - +
87A ALA* 3.3 7.5 + - - +
88A ASP* 3.2 18.2 + - - +
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Residues in contact with PHE 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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29A LEU* 3.7 28.5 - - + -
32A PHE* 3.7 12.3 - + + -
33A LEU* 3.9 26.2 - - + -
36A LEU* 3.9 11.7 - - + -
70A MET* 3.6 27.2 - - + +
74A ILE* 3.9 22.2 - - + -
79A TYR* 3.6 35.3 - + + -
81A SER 3.3 5.7 + - - +
82A VAL* 3.1 9.3 + - + +
84A GLU* 1.3 78.6 - - - +
86A LYS* 1.3 64.8 + - + +
88A ASP* 3.2 5.7 + - - +
89A PHE* 3.1 17.6 + - + +
121A MET* 3.7 29.6 - - + -
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Residues in contact with LYS 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 VAL* 2.8 36.6 + - + +
83A THR* 3.7 7.9 - - - +
85A PHE* 1.3 77.9 - - + +
87A ALA* 1.3 56.8 + - - +
89A PHE* 3.2 5.9 + - - +
90A LYS 2.8 25.5 + - - -
118A PHE* 3.5 41.2 - - + -
121A MET* 3.9 36.3 + - + -
122A SER* 2.9 34.3 + - - +
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Residues in contact with ALA 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 THR* 3.0 19.4 + - + +
84A GLU* 3.6 8.3 - - - +
85A PHE 3.2 0.2 - - - -
86A LYS* 1.3 76.5 - - - +
88A ASP* 1.3 58.5 + - - +
90A LYS* 3.4 7.3 + - - +
91A LEU* 2.9 28.6 + - - +
118A PHE* 5.4 0.2 - - - -
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Residues in contact with ASP 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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65A MET* 3.5 30.9 - - + +
70A MET* 4.1 10.1 - - + -
73A LYS* 2.8 28.2 + - - +
79A TYR* 2.7 33.5 + - - +
84A GLU 3.2 7.7 + - - +
85A PHE 3.2 7.8 + - - +
87A ALA* 1.3 74.9 - - - +
89A PHE* 1.3 66.5 + - - +
91A LEU* 3.3 11.6 + - - +
92A MET* 3.0 19.4 + - - +
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Residues in contact with PHE 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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36A LEU* 3.7 27.8 - - + -
67A PHE* 4.0 11.9 - + - -
70A MET* 3.7 14.7 - - + +
85A PHE* 3.1 13.1 + - + +
86A LYS* 3.6 8.7 - - - +
88A ASP* 1.3 76.4 - - - +
90A LYS* 1.3 62.0 + - - +
92A MET* 3.2 31.1 + - + +
93A CYS* 3.1 32.1 + - - -
113A ILE* 3.3 40.4 - - + -
114A LEU* 3.9 15.5 - - + -
117A GLY* 4.0 11.9 - - - -
118A PHE* 3.8 19.1 - + - -
121A MET* 3.8 10.5 - - + -
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Residues in contact with LYS 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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86A LYS 2.8 21.1 + - - +
87A ALA* 3.8 6.1 - - - +
89A PHE* 1.3 74.7 - - - +
91A LEU* 1.3 57.0 + - - +
93A CYS* 3.2 1.6 + - - +
94A ASP* 2.7 62.0 + - - +
114A LEU* 3.9 22.4 - - + -
118A PHE* 3.8 21.5 - - + -
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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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63A HIS* 3.4 45.1 - - + +
64A PRO 4.5 1.6 - - - +
65A MET* 4.1 17.5 - - + -
87A ALA 2.9 18.4 + - - +
88A ASP* 3.5 17.0 - - - +
90A LYS* 1.3 76.1 - - - +
92A MET* 1.3 56.7 + - - +
94A ASP* 3.7 6.2 - - + -
95A ASN* 2.8 53.8 + - - +
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Residues in contact with MET 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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45A PHE* 3.5 41.4 - - + -
65A MET* 3.5 29.3 - - + +
66A ASP* 3.7 4.0 - - - -
67A PHE* 3.6 60.8 - - + -
70A MET* 4.6 2.5 - - - +
88A ASP 3.0 12.8 + - - +
89A PHE* 3.2 26.2 + - + +
91A LEU* 1.3 77.5 - - - +
93A CYS* 1.3 67.0 + - - +
95A ASN* 3.4 5.2 + - - +
96A ALA* 3.2 21.1 + - - +
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Residues in contact with CYS 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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45A PHE* 4.4 3.8 - - - -
89A PHE* 3.1 47.4 + - - +
90A LYS 3.8 4.7 - - - +
92A MET* 1.3 78.5 - - - +
94A ASP* 1.3 61.7 + - - +
96A ALA* 3.2 3.8 + - - +
97A MET* 2.9 36.7 + - + +
110A ALA* 3.6 24.4 - - - +
113A ILE* 3.9 10.8 - - - -
114A LEU* 3.8 25.1 - - + -
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Residues in contact with ASP 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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90A LYS* 2.7 56.0 + - - +
91A LEU* 3.8 7.8 + - + +
93A CYS* 1.3 73.8 - - - +
95A ASN* 1.4 63.0 + - - +
97A MET* 3.1 20.7 + - - +
98A THR* 2.9 30.0 + - - +
114A LEU* 3.9 10.7 - - - +
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Residues in contact with ASN 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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57A TYR* 3.6 17.6 + - - +
61A ILE* 3.5 33.1 - - + +
63A HIS 2.8 26.4 + - - +
64A PRO* 3.6 8.7 - - - +
65A MET 3.7 8.4 - - - +
91A LEU* 2.8 34.4 + - - +
92A MET* 3.6 5.9 - - - +
93A CYS 3.3 0.2 - - - -
94A ASP* 1.4 75.5 - - - +
96A ALA* 1.3 58.1 + - - +
98A THR* 3.3 2.3 + - - -
99A TYR* 2.8 33.4 + - - +
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Residues in contact with ALA 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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45A PHE* 3.9 4.7 - - + -
57A TYR* 4.7 1.5 + - - -
92A MET 3.2 10.2 + - - +
93A CYS 3.2 8.8 + - - +
95A ASN* 1.3 78.9 - - - +
97A MET* 1.3 60.0 + - - +
99A TYR* 5.0 0.4 - - - -
100A ASN* 2.9 42.1 + - - +
106A TYR 4.4 1.3 - - - +
107A TYR* 4.5 1.7 - - - -
110A ALA* 3.5 19.1 - - + -
5Z KCR 3.8 29.8 - - + +
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Residues in contact with MET 97 (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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93A CYS* 2.9 29.4 + - + +
94A ASP* 3.1 16.5 + - - +
96A ALA* 1.3 77.7 - - - +
98A THR* 1.3 60.9 + - - +
100A ASN 3.4 4.9 - - - +
107A TYR* 3.3 48.4 - - + +
110A ALA* 3.8 16.8 - - + +
111A LYS* 3.7 28.7 - - - -
114A LEU* 3.6 31.0 - - + -
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Residues in contact with THR 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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60A ILE* 3.9 15.5 - - + +
61A ILE* 3.9 19.1 - - + -
94A ASP* 2.9 19.8 + - - +
95A ASN* 3.6 3.3 - - - -
97A MET* 1.3 80.0 - - - +
99A TYR* 1.4 62.3 + - - +
100A ASN 4.3 1.2 - - - +
3Z ARG* 2.8 23.1 + - - +
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Residues in contact with TYR 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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54A ALA* 3.1 31.7 - - + -
55A PRO* 2.7 29.8 + - - +
57A TYR* 3.5 40.8 - + + -
60A ILE* 3.8 21.3 - - + -
61A ILE* 4.4 4.5 - - + -
95A ASN 2.8 20.0 + - - +
98A THR* 1.4 77.9 - - - +
100A ASN* 1.3 78.9 + - - +
101A ARG 4.0 0.7 + - - -
3Z ARG* 2.9 45.3 + - + +
4Z GLY* 3.2 38.3 + - - -
5Z KCR 4.3 2.7 - - - -
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Residues in contact with ASN 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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96A ALA* 2.9 28.9 + - - +
97A MET 3.4 6.9 - - - +
98A THR 4.3 1.3 - - - +
99A TYR* 1.3 92.5 - - - +
101A ARG* 1.3 64.7 + - - +
102A PRO* 3.8 1.0 - - - +
104A THR* 3.4 17.9 - - + +
106A TYR* 3.6 23.7 - - - +
107A TYR* 3.4 20.9 - - - +
3Z ARG 5.3 2.9 - - - -
4Z GLY* 4.7 2.0 - - - -
5Z KCR 2.9 46.2 + - - +
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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