Contacts of the helix formed by residues 64 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLN* 3.1 32.3 + - + +
28A LEU* 3.9 30.1 - - + -
59A GLY 3.0 7.4 + - - +
62A LEU* 3.1 23.2 + - + +
63A LYS* 1.3 73.2 + - - +
65A GLY* 1.3 64.3 + - - +
66A LYS* 3.3 3.1 + - + -
67A LEU* 3.4 13.9 + - + +
68A LEU* 3.2 26.6 + - - +
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Residues in contact with GLY 65 (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 LYS 3.1 9.5 + - - -
64A LYS* 1.3 74.4 - - - +
66A LYS* 1.3 56.6 + - - +
68A LEU* 3.3 9.3 + - - +
69A LYS* 2.9 30.5 + - - +
96A PHE* 5.9 1.0 - - - -
157A PHE* 3.6 19.9 - - - -
160A GLU* 5.8 2.5 - - - -
161A SER* 5.7 1.6 - - - -
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Residues in contact with LYS 66 (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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64A LYS* 3.3 1.0 - - + -
65A GLY* 1.3 76.2 - - - +
67A LEU* 1.3 63.2 + - - +
69A LYS* 3.3 17.4 + - - +
70A ASP* 3.1 23.1 + - - +
339C GLU* 3.4 33.4 + - - -
431C ARG* 4.2 8.7 - - - +
434C VAL* 5.4 11.9 - - - +
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Residues in contact with LEU 67 (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 GLN 6.0 0.2 - - - +
28A LEU* 3.9 33.9 - - + +
29A GLN* 3.9 23.1 - - - +
32A HIS* 3.5 38.1 - - + +
55A PHE* 3.7 10.3 - - + -
64A LYS* 3.4 18.8 + - + +
65A GLY 3.4 0.2 - - - -
66A LYS* 1.3 78.8 - - - +
68A LEU* 1.3 57.6 + - - +
70A ASP* 3.4 6.8 + - + +
71A GLY* 2.9 27.5 + - - -
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Residues in contact with LEU 68 (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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28A LEU* 6.0 0.4 - - + -
55A PHE* 3.6 42.5 - - + +
56A LEU* 4.1 15.9 - - + -
59A GLY* 3.7 28.3 - - - +
60A VAL* 3.9 3.8 - - + +
64A LYS 3.2 19.8 + - - +
65A GLY* 3.4 7.4 - - - +
67A LEU* 1.3 77.1 - - - +
69A LYS* 1.3 62.4 + - - +
71A GLY* 3.1 2.6 + - - -
72A LEU* 3.0 30.1 + - + +
96A PHE* 3.7 36.3 - - + -
157A PHE* 4.1 10.8 - - + -
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 2.9 16.7 + - - +
66A LYS* 3.7 14.8 - - - +
68A LEU* 1.3 76.7 - - - +
70A ASP* 1.3 66.8 + - - +
72A LEU* 3.4 5.8 + - - +
73A HIS* 3.2 42.7 + - + +
96A PHE* 5.8 2.4 - - - -
164A ALA* 4.0 31.2 - - + -
339C GLU* 4.0 27.6 + - - +
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Residues in contact with ASP 70 (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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32A HIS* 3.7 13.0 + - - +
66A LYS 3.1 15.9 + - - +
67A LEU* 3.8 7.9 - - + +
69A LYS* 1.3 81.1 - - - +
71A GLY* 1.3 61.5 + - - +
73A HIS* 4.1 3.6 - - - +
74A GLN* 3.1 42.4 + - - +
364C LYS* 3.6 28.6 + - - +
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Residues in contact with GLY 71 (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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32A HIS* 4.1 18.1 + - - -
35A ILE* 4.6 5.9 - - - +
36A THR* 4.5 8.0 - - - +
55A PHE* 4.3 7.9 - - - -
67A LEU 2.9 15.2 + - - -
68A LEU 3.1 4.0 + - - -
70A ASP* 1.3 77.7 + - - +
72A LEU* 1.3 58.2 + - - +
74A GLN* 3.8 1.4 - - - +
75A TYR* 2.9 32.2 + - - +
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Residues in contact with LEU 72 (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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35A ILE* 5.8 0.2 - - + -
52A VAL* 4.6 11.7 - - + -
55A PHE* 4.7 2.9 - - + -
56A LEU* 3.7 28.3 - - + -
68A LEU* 3.0 18.8 + - + +
69A LYS* 3.9 5.4 - - - +
70A ASP 3.4 0.4 - - - -
71A GLY* 1.3 76.2 - - - +
73A HIS* 1.3 58.4 + - - +
75A TYR* 3.3 7.5 + - + +
76A LYS* 2.9 30.1 + - - +
92A VAL* 4.7 14.8 - - + +
93A ALA* 4.8 8.1 - - - -
96A PHE* 3.8 35.4 - - + -
165A VAL* 4.9 3.6 - - + -
168A LEU* 3.8 29.7 - - + +
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Residues in contact with HIS 73 (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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69A LYS* 3.2 41.2 + - + +
70A ASP* 4.1 3.8 - - - +
72A LEU* 1.3 79.1 - - - +
74A GLN* 1.3 62.7 + - - +
76A LYS* 3.2 4.7 + - + +
77A LYS* 3.0 48.9 + - - +
164A ALA 4.4 8.1 - - - -
167A ASP* 3.9 23.5 + - + -
168A LEU* 3.8 35.6 - - + +
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Residues in contact with GLN 74 (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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32A HIS* 4.3 4.9 - - - -
36A THR* 3.4 46.3 + - + +
70A ASP* 3.1 35.2 + - - +
71A GLY 3.8 2.5 - - - +
73A HIS* 1.3 77.0 - - - +
75A TYR* 1.3 63.3 + - - +
77A LYS* 3.4 10.1 + - + +
78A LEU* 3.4 26.0 + - + +
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Residues in contact with TYR 75 (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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35A ILE* 3.9 32.1 - - + +
36A THR* 5.1 0.6 - - - +
40A ILE* 4.3 17.7 - - + -
45A PRO* 4.0 9.6 + - + +
48A VAL* 4.6 6.1 - - + -
49A GLU 5.0 0.9 + - - -
52A VAL* 4.4 25.6 - - + -
71A GLY 2.9 19.2 + - - +
72A LEU* 3.7 6.7 - - - +
74A GLN* 1.3 76.3 - - - +
76A LYS* 1.3 66.4 + - - +
78A LEU* 3.2 5.1 + - + +
79A ILE* 3.1 54.2 + - + +
88A SER* 2.6 33.3 + - - -
89A VAL* 4.2 13.5 - - + -
92A VAL* 4.4 19.7 - - + -
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Residues in contact with LYS 76 (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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72A LEU 2.9 13.9 + - - +
73A HIS* 3.4 9.2 - - - +
75A TYR* 1.3 78.1 - - - +
77A LYS* 1.3 76.5 + - - +
80A GLN* 2.9 63.3 + - + +
89A VAL* 3.9 31.9 - - + -
168A LEU* 3.5 41.7 - - + +
172A ASN* 4.6 16.8 - - - +
175A LEU* 5.0 3.4 - - - -
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Residues in contact with LYS 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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41A ARG* 3.3 22.5 + - - +
73A HIS* 3.0 45.9 + - - +
74A GLN* 3.7 11.7 - - + +
75A TYR 3.3 0.4 - - - -
76A LYS* 1.3 95.3 - - - +
78A LEU* 1.3 60.9 + - + +
80A GLN* 3.9 29.8 + - - +
365C GLU* 5.5 6.5 - - - -
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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
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35A ILE 3.8 20.2 - - - +
36A THR* 3.9 13.2 - - - +
37A ALA 3.2 28.7 - - - +
38A ARG* 4.0 12.8 - - + -
40A ILE* 4.4 6.1 - - + -
41A ARG* 3.4 72.8 + - + +
74A GLN* 3.4 18.6 + - + +
75A TYR* 3.2 6.8 + - - +
76A LYS 3.2 0.6 - - - -
77A LYS* 1.3 77.8 - - + +
79A ILE* 1.3 61.9 + - + +
80A GLN 3.6 0.2 - - - -
81A GLY* 4.8 2.3 + - - -
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Residues in contact with ILE 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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40A ILE* 4.2 13.5 - - + +
41A ARG 4.9 4.5 - - - +
43A ALA 4.1 10.1 - - - +
45A PRO* 3.6 37.5 - - + -
75A TYR* 3.1 50.6 + - + +
76A LYS 3.8 0.4 - - - +
78A LEU* 1.3 77.4 - - + +
80A GLN* 1.3 61.2 + - - +
81A GLY 2.8 12.9 + - - -
82A SER* 3.5 7.2 + - - +
85A GLY* 3.3 28.7 - - - +
89A VAL* 3.7 18.6 - - + -
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Residues in contact with GLN 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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76A LYS* 2.9 52.9 + - + +
77A LYS* 3.9 30.2 + - - +
78A LEU 3.6 0.2 - - - -
79A ILE* 1.3 77.0 - - - +
81A GLY* 1.3 64.4 + - - +
82A SER 3.4 0.9 - - - -
86A LEU* 3.1 34.4 - - + +
89A VAL* 5.5 1.3 - - + -
172A ASN* 5.6 2.6 + - - +
223A ASN* 4.8 5.0 + - - -
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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