Contacts of the helix formed by residues 76 - 97 (chain A) in PDB entry 2LUC
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.4 5.6 - - - -
31A ASN 6.0 0.2 - - - +
32A TYR 4.5 0.4 - - - +
33A THR* 3.3 17.6 - - + +
70A ASN* 5.6 4.0 - - + +
75A LEU* 1.3 75.1 - - - +
77A PHE* 1.3 77.1 + - + +
78A SER* 2.6 29.1 + - - -
79A GLU* 2.7 42.1 + - - +
80A PHE* 2.7 30.3 + - - +
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Residues in contact with PHE 77 (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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21A PHE* 3.3 22.9 - + - -
22A GLN* 4.0 2.9 - - - -
31A ASN 3.8 17.3 - - - -
32A TYR* 3.6 23.3 - - + -
76A ASP* 1.3 90.3 - - + +
78A SER* 1.3 58.0 + - - +
80A PHE* 3.8 2.9 - - - +
81A LEU* 2.9 32.8 + - - +
89B MET* 4.6 13.7 - - + -
92B HIS* 3.2 42.5 + + + -
96B LEU* 3.5 37.5 - - + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 2.6 23.7 + - - -
77A PHE* 1.3 77.6 - - - +
79A GLU* 1.3 54.8 + - - +
81A LEU* 3.1 7.6 + - - +
82A ASN* 2.7 42.6 + - - +
89B MET* 3.3 30.5 - - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.5 0.9 - - - +
67A LEU* 3.2 27.2 - - - +
68A ASP* 3.2 5.5 - - - -
69A THR* 2.6 41.8 + - + -
70A ASN* 2.7 28.8 + - - +
74A GLN 3.6 7.8 - - - +
75A LEU* 3.7 10.3 - - + -
76A ASP* 2.7 51.6 + - - +
78A SER* 1.3 73.2 - - - +
80A PHE* 1.3 65.5 + - - +
82A ASN* 3.3 11.4 - - - +
83A LEU* 3.1 16.8 + - - +
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Residues in contact with PHE 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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17A LEU* 3.9 17.3 - - + -
20A VAL* 3.4 23.1 - - + -
21A PHE* 3.4 37.7 - + + -
34A LEU* 3.8 17.3 - - + -
39A PHE* 4.5 2.5 - + - -
42A PHE* 3.2 31.6 - + - -
75A LEU* 4.0 8.8 - - + +
76A ASP 2.7 19.9 + - - +
77A PHE 3.8 2.2 - - - +
79A GLU* 1.3 73.4 - - - +
81A LEU* 1.3 69.0 + - + +
83A LEU* 2.9 24.6 - - + +
84A ILE* 2.9 47.9 + - + +
92B HIS* 5.4 1.1 - - - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.4 35.7 - - + -
77A PHE 2.9 21.5 - - - +
78A SER* 3.1 7.1 + - - +
80A PHE* 1.3 88.3 - - + +
82A ASN* 1.3 61.0 + - - +
83A LEU 3.1 0.4 - - - -
84A ILE* 3.4 6.7 - - + +
85A GLY* 2.8 24.6 + - - -
81B LEU 5.5 2.4 - - - +
84B ILE* 5.2 2.0 - - + +
85B GLY* 3.4 29.1 - - - +
88B ALA* 3.3 30.5 - - + -
89B MET* 3.8 12.3 - - + +
92B HIS* 4.7 6.3 - - + +
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Residues in contact with ASN 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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67A LEU* 3.8 23.3 + - + +
69A THR* 5.0 8.5 - - - +
78A SER* 2.7 25.7 + - - +
79A GLU* 3.3 19.1 - - - +
81A LEU* 1.3 72.8 - - - +
83A LEU* 1.3 61.8 + - - +
85A GLY* 3.1 10.8 + - - +
86A GLY* 3.1 10.4 + - - -
82B ASN* 5.7 1.2 - - - +
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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
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39A PHE* 3.5 32.8 - - + -
43A MET* 4.6 0.2 - - + -
47A LEU* 4.0 8.7 - - + -
63A MET* 3.6 31.3 - - + +
67A LEU* 3.3 27.5 - - + +
79A GLU 3.1 2.8 + - - -
80A PHE* 2.9 37.0 - - + +
82A ASN* 1.3 76.6 - - - +
84A ILE* 1.3 53.4 + - - +
86A GLY* 2.8 5.9 + - - -
87A LEU* 2.8 58.1 + - + +
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Residues in contact with ILE 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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17A LEU* 3.5 36.3 - - + -
47A LEU* 5.6 0.2 - - + -
80A PHE* 2.9 38.6 + - + +
81A LEU* 3.2 14.6 + - + +
83A LEU* 1.3 75.5 - - + +
85A GLY* 1.3 56.0 + - - +
87A LEU* 3.6 16.1 - - + +
88A ALA* 2.8 29.5 + - - +
10B THR* 3.1 27.6 - - - +
13B CYS* 4.3 2.9 - - - -
14B ILE* 4.1 14.6 - - + -
17B LEU* 4.6 10.8 - - + -
81B LEU* 5.6 1.6 - - + -
84B ILE* 5.4 3.4 - - + -
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Residues in contact with GLY 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 LEU 2.8 14.1 + - - -
82A ASN* 3.1 6.3 + - - -
83A LEU 3.0 0.6 - - - -
84A ILE* 1.3 76.5 - - - +
86A GLY* 1.3 56.5 + - - +
89A MET* 2.9 42.6 + - - +
81B LEU* 3.4 23.9 - - - +
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Residues in contact with GLY 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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50A PHE* 5.9 0.4 - - - -
63A MET* 6.6 0.4 - - - -
66A LYS* 5.8 5.4 - - - -
82A ASN 3.1 7.9 + - - -
83A LEU* 2.8 10.4 + - - -
85A GLY* 1.3 70.7 - - - -
87A LEU* 1.3 59.1 + - - +
89A MET* 3.4 16.6 + - - +
90A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 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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43A MET* 5.1 0.2 - - + -
47A LEU* 3.4 47.6 - - + -
50A PHE* 4.0 37.5 - - + -
63A MET* 5.2 1.6 - - + -
83A LEU* 2.8 38.2 + - + +
84A ILE* 3.6 17.7 - - + +
86A GLY* 1.3 74.0 - - - +
88A ALA* 1.3 65.0 + - - +
90A ALA* 3.0 8.2 + - - +
91A CYS* 3.0 22.3 + - - +
14B ILE* 3.4 15.7 - - + -
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Residues in contact with ALA 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 ILE 2.8 22.6 + - - +
87A LEU* 1.3 72.5 - - - +
89A MET* 1.3 54.1 + - - +
91A CYS* 3.3 1.0 + - - +
92A HIS* 2.7 46.7 + - + -
14B ILE* 3.2 27.8 - - + +
17B LEU* 4.7 4.7 - - + -
81B LEU* 3.3 29.2 - - + -
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Residues in contact with MET 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 GLY* 2.9 30.9 + - - +
86A GLY* 3.7 15.5 - - - +
87A LEU 3.2 0.2 - - - -
88A ALA* 1.3 76.9 - - - +
90A ALA* 1.3 57.8 + - - +
92A HIS* 3.7 7.0 - - - +
93A ASP* 2.8 30.3 + - - +
76B ASP* 5.9 0.2 - - - +
77B PHE* 4.6 7.6 - - + -
78B SER* 3.3 36.3 - - - +
81B LEU* 3.8 12.3 - - + -
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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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50A PHE* 4.6 21.8 - - + -
86A GLY 2.9 14.2 + - - +
87A LEU* 3.0 11.2 + - - +
89A MET* 1.3 77.9 - - - +
91A CYS* 1.3 53.3 + - - +
93A ASP* 3.4 7.0 + - - +
94A SER* 2.7 35.9 + - - -
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Residues in contact with CYS 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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87A LEU 3.0 13.9 + - - +
88A ALA 3.9 2.7 - - - +
90A ALA* 1.3 74.0 - - - +
92A HIS* 1.3 66.8 + - - +
94A SER* 3.1 12.0 - - - -
95A PHE* 3.0 38.8 + - - -
14B ILE* 4.0 9.6 - - + -
15B GLU* 4.1 20.4 - - - -
18B ILE* 3.4 23.6 - - + -
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Residues in contact with HIS 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 ALA* 2.7 40.4 + - + +
89A MET* 3.7 8.3 - - - +
91A CYS* 1.3 72.3 - - - +
93A ASP* 1.3 51.1 + - - +
95A PHE* 2.8 5.2 + - - +
96A LEU* 2.7 40.1 + - - +
17B LEU* 4.0 8.4 + - - +
18B ILE* 3.3 45.1 + - + +
21B PHE* 3.6 27.2 - + + +
22B GLN* 2.7 23.5 + - - -
77B PHE* 3.2 27.3 + + + +
80B PHE* 5.5 0.4 - - - -
81B LEU* 4.7 10.2 - - + +
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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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89A MET 2.8 20.8 + - - +
90A ALA* 3.5 8.2 - - - +
92A HIS* 1.3 74.9 - - - +
94A SER* 1.3 59.2 + - - +
96A LEU* 3.2 8.3 + - - +
97A LYS* 2.8 57.8 + - - +
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Residues in contact with SER 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 ALA 2.7 20.7 + - - -
91A CYS* 3.1 18.0 - - - -
93A ASP* 1.3 77.2 + - - +
95A PHE* 1.3 60.8 + - - +
97A LYS* 3.2 8.3 + - - +
98A ALA* 3.0 29.4 + - - +
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Residues in contact with PHE 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 CYS* 3.0 33.5 + - - +
92A HIS 2.8 8.8 + - - +
94A SER* 1.3 76.7 - - - +
96A LEU* 1.3 61.0 + - - +
98A ALA* 2.9 7.9 + - + -
99A VAL* 2.6 55.2 + - + +
100A PRO* 3.0 9.5 - - + -
102A GLN* 3.8 25.1 - - + -
15B GLU* 4.8 12.1 - - + -
18B ILE* 3.7 26.7 - - + -
22B GLN* 4.1 21.5 - - - +
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Residues in contact with LEU 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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92A HIS 2.7 32.9 + - - +
93A ASP* 3.2 11.4 + - - +
95A PHE* 1.3 72.1 - - - +
97A LYS* 1.3 74.9 + - - +
98A ALA 3.2 2.4 + - - -
100A PRO* 3.6 36.3 - - + +
22B GLN* 3.9 5.8 - - - +
31B ASN 5.6 0.4 - - - +
32B TYR* 3.8 18.4 - - + -
77B PHE* 3.5 38.8 - - + -
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Residues in contact with LYS 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 ASP* 2.8 48.6 + - - +
94A SER* 3.3 6.3 - - - +
95A PHE 3.1 0.2 - - - -
96A LEU* 1.3 95.2 + - - +
98A ALA* 1.3 57.8 + - - +
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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