Contacts of the helix formed by residues 64 - 80 (chain C) in PDB entry 4U1D
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLN* 2.9 43.9 + - - +
28C LEU* 3.6 33.0 - - + -
59C GLY 3.0 7.3 + - - +
62C LEU* 3.8 21.8 - - + +
63C LYS* 1.3 73.9 - - - +
65C GLY* 1.3 63.8 + - - +
66C LYS 3.3 2.9 + - - -
67C LEU* 3.3 13.2 + - + +
68C LEU* 3.1 25.9 + - - +
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Residues in contact with GLY 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS 3.1 9.1 + - - -
64C LYS* 1.3 74.4 - - - +
66C LYS* 1.3 62.1 + - - +
68C LEU* 3.5 8.5 + - - +
69C LYS* 3.1 33.7 + - - +
96C PHE* 5.9 1.2 - - - -
157C PHE* 3.8 17.9 - - - -
160C GLU* 6.5 1.8 - - - -
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 5.4 5.9 + - - -
461B SER* 5.9 2.9 - - - -
463B TRP* 5.6 0.3 - - - -
64C LYS 3.3 0.8 - - - -
65C GLY* 1.3 71.9 - - - +
67C LEU* 1.3 61.8 + - - +
69C LYS* 3.2 14.1 + - - +
70C ASP* 2.9 30.8 + - - +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN* 5.7 2.2 - - + +
28C LEU* 3.6 35.4 - - + -
29C GLN* 3.9 24.2 - - + +
32C HIS* 3.4 39.6 - - + +
55C PHE* 3.4 11.0 - - + -
64C LYS* 3.3 18.8 + - + +
66C LYS* 1.3 78.3 - - - +
68C LEU* 1.3 54.1 + - - +
70C ASP* 3.7 5.6 - - + +
71C GLY 2.8 29.1 + - - -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 5.9 0.2 - - + -
55C PHE* 3.9 26.2 - - + +
56C LEU* 4.0 20.6 - - + +
59C GLY* 3.7 41.1 - - - +
60C VAL 4.1 1.6 - - - +
64C LYS 3.1 16.1 + - - +
65C GLY* 3.6 8.5 - - - +
67C LEU* 1.3 77.0 - - - +
69C LYS* 1.3 56.9 + - - +
71C GLY* 3.2 1.7 + - - -
72C LEU* 3.0 36.5 + - + +
96C PHE* 3.4 36.3 - - + -
157C PHE* 4.0 15.3 - - + -
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TRP* 3.8 30.1 - - + +
65C GLY* 3.1 18.5 + - - +
66C LYS* 3.5 14.2 - - - +
68C LEU* 1.3 77.9 - - - +
70C ASP* 1.3 59.7 + - - +
72C LEU* 3.4 8.1 + - - +
73C HIS* 3.0 45.2 + - + +
96C PHE* 5.8 1.5 - - - -
160C GLU* 3.5 29.0 + - - +
163C ARG* 6.0 0.2 - - - +
164C ALA* 3.7 35.5 - - + +
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Residues in contact with ASP 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TRP* 4.1 23.7 - - + -
32C HIS* 3.0 21.2 + - - +
66C LYS 2.9 16.6 + - - +
67C LEU* 3.8 8.1 - - + +
69C LYS* 1.3 73.8 - - - +
71C GLY* 1.3 66.9 + - - +
74C GLN* 2.9 55.3 + - - +
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Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C HIS* 3.7 19.2 + - - -
35C ILE* 4.4 4.0 - - - +
36C THR* 4.1 6.7 - - - +
55C PHE* 4.0 10.1 - - - -
67C LEU 2.8 18.7 + - - -
68C LEU 3.6 1.8 - - - -
70C ASP* 1.3 76.8 - - - +
72C LEU* 1.3 56.8 + - - +
74C GLN* 4.0 0.9 - - - +
75C TYR* 2.9 33.5 + - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 4.5 5.8 - - + -
55C PHE* 5.5 0.2 - - + -
56C LEU* 3.9 17.5 - - + -
68C LEU* 3.0 23.0 + - + +
69C LYS* 3.8 6.7 - - - +
71C GLY* 1.3 74.7 - - - +
73C HIS* 1.3 58.5 + - - +
75C TYR* 3.3 7.0 + - + +
76C LYS* 2.8 32.4 + - - +
92C VAL* 3.4 33.0 - - + +
93C ALA* 5.4 2.2 - - - -
96C PHE* 3.8 36.3 - - + -
164C ALA* 6.3 2.0 - - + -
165C VAL* 5.1 4.3 - - + -
168C LEU* 3.7 28.2 - - + +
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TRP* 3.4 70.9 - + + +
69C LYS* 3.0 33.2 + - + +
70C ASP 4.3 0.7 - - - +
72C LEU* 1.3 76.6 - - - +
74C GLN* 1.3 64.1 + - - +
76C LYS* 3.3 3.4 + - + +
77C LYS* 3.1 34.6 + - + +
164C ALA 4.5 3.8 - - - -
167C ASP* 4.1 6.2 + - + -
168C LEU* 3.4 50.1 - - + +
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Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C HIS* 4.1 4.1 - - - -
36C THR* 3.5 44.2 + - + +
70C ASP* 2.9 40.4 + - - +
73C HIS* 1.3 75.8 - - - +
75C TYR* 1.3 62.2 + - - +
77C LYS* 3.5 9.2 + - + +
78C LEU* 3.4 26.2 + - + +
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.6 32.1 - - + +
36C THR* 4.6 0.8 - - - +
40C ILE* 4.1 9.6 - - + -
45C PRO* 4.0 10.7 + - - +
48C VAL* 4.4 6.3 - - + -
49C GLU* 4.4 2.8 + - - -
52C VAL* 3.8 36.2 - - + +
71C GLY 2.9 22.1 + - - +
72C LEU* 3.6 6.5 - - + +
74C GLN* 1.3 74.8 - - - +
76C LYS* 1.3 68.2 + - + +
78C LEU* 3.1 7.5 + - - +
79C ILE* 3.0 53.0 + - + +
88C SER* 2.7 32.0 + - - -
89C VAL* 4.6 11.0 - - + -
92C VAL* 4.5 13.9 - - + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU 2.8 21.2 + - - +
73C HIS* 3.7 6.1 - - + +
75C TYR* 1.3 73.7 - - + +
77C LYS* 1.3 67.3 + - + +
79C ILE 3.0 0.4 + - - +
80C GLN* 2.7 65.0 + - + +
86C LEU* 4.9 2.0 - - - -
89C VAL* 3.7 38.6 - - + -
168C LEU* 3.7 38.9 + - + +
172C ASN* 4.5 10.6 - - - +
175C LEU* 4.4 17.0 - - - -
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLN* 4.2 24.9 + - - +
466B GLU* 5.4 1.2 + - - -
484B HIS* 4.4 14.3 + - - -
487B ALA* 5.9 4.6 - - - +
41C ARG* 3.3 23.3 + - - +
73C HIS* 3.1 27.9 + - + +
74C GLN* 3.7 9.4 - - + +
75C TYR 3.2 0.4 - - - -
76C LYS* 1.3 84.6 - - + +
78C LEU* 1.3 59.8 + - + +
80C GLN* 3.0 41.8 + - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE 4.0 7.0 - - - +
36C THR* 3.7 24.9 - - - +
37C ALA 3.3 26.7 - - - +
38C ARG* 4.2 9.4 - - - +
40C ILE* 4.2 6.3 - - + -
41C ARG* 3.3 73.2 + - + +
74C GLN* 3.4 19.0 + - + +
75C TYR* 3.1 6.9 + - - +
76C LYS 3.1 0.6 - - - -
77C LYS* 1.3 80.4 - - + +
79C ILE* 1.3 59.4 + - + +
80C GLN 3.7 0.2 - - - -
81C GLY* 4.8 1.6 + - - -
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.3 30.7 - - + +
41C ARG 4.9 2.9 - - - +
43C ALA* 4.0 14.6 - - + +
45C PRO* 4.3 18.2 - - + -
48C VAL* 6.2 0.2 - - + -
75C TYR* 3.0 50.9 + - + +
76C LYS* 3.0 2.3 + - - +
78C LEU* 1.3 80.5 - - - +
80C GLN* 1.3 53.6 + - - +
81C GLY 2.8 16.6 + - - -
82C SER* 3.6 5.8 + - - +
85C GLY* 3.2 41.7 - - - +
89C VAL* 4.4 5.6 - - + -
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B HIS* 4.0 22.4 + - - +
41C ARG* 5.9 0.9 - - - +
76C LYS* 2.7 53.9 + - + +
77C LYS* 3.0 44.5 + - - +
78C LEU 3.7 0.2 - - - -
79C ILE* 1.3 74.9 - - - +
81C GLY* 1.3 61.9 + - - +
82C SER 3.4 6.2 - - - +
85C GLY 4.6 0.2 - - - -
86C LEU* 3.6 35.6 - - + +
89C VAL* 5.2 0.4 - - - -
172C ASN* 5.3 1.7 + - - -
223C ASN* 4.8 5.7 + - - -
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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