Contacts of the helix formed by residues 64 - 80 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN* 3.3 35.2 - - + +
28B LEU* 3.8 24.9 - - + -
59B GLY* 3.0 7.9 + - - +
62B LEU* 3.1 34.0 + - + +
63B LYS* 1.3 73.8 + - - +
65B GLY* 1.3 63.0 + - - +
66B LYS* 3.3 3.4 + - - -
67B LEU* 3.3 12.4 + - + -
68B LEU* 3.1 25.6 + - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS 3.1 8.9 + - - -
64B LYS* 1.3 74.8 - - - +
66B LYS* 1.3 62.6 + - - +
68B LEU* 3.2 8.5 + - - +
69B LYS* 2.9 39.4 + - - +
96B PHE* 5.8 2.0 - - - -
157B PHE* 3.8 17.6 - - - -
161B SER* 6.1 0.2 - - - -
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS 3.3 1.2 - - - -
65B GLY* 1.3 76.1 - - - +
67B LEU* 1.3 63.3 + - - +
69B LYS* 3.3 10.5 + - + +
70B ASP* 3.1 22.9 + - - +
459C ASP* 5.6 3.8 + - - -
463C TRP* 5.0 1.9 - - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.7 34.3 - - + -
29B GLN* 3.7 25.6 - - + +
32B HIS* 3.4 40.8 - - + +
55B PHE* 3.6 11.1 - - + -
64B LYS* 3.3 18.8 + - + +
66B LYS* 1.3 78.1 - - - +
68B LEU* 1.3 52.9 + - - +
70B ASP* 3.4 4.8 + - + -
71B GLY* 2.7 32.1 + - - -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 6.0 0.4 - - + -
55B PHE* 3.9 21.3 - - + +
56B LEU* 3.7 27.1 - - + -
59B GLY* 3.6 42.6 - - - +
60B VAL 3.9 2.0 - - - +
64B LYS 3.1 16.4 + - - +
65B GLY* 3.4 8.5 - - - +
66B LYS 3.2 0.2 - - - -
67B LEU* 1.3 74.4 - - + +
69B LYS* 1.3 65.9 + - - +
71B GLY* 3.2 0.9 + - - -
72B LEU* 3.0 31.3 + - - +
96B PHE* 3.7 33.7 - - + -
157B PHE* 4.1 12.8 - - + -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 2.9 28.5 + - - +
66B LYS* 3.7 11.2 - - + +
68B LEU* 1.3 74.5 - - + +
70B ASP* 1.3 58.1 + - - +
72B LEU* 3.4 6.0 + - - +
73B HIS* 2.9 36.9 + - - +
96B PHE* 5.6 4.5 - - + -
160B GLU* 3.0 43.4 + - - +
161B SER* 5.5 0.9 - - - +
163B ARG* 5.0 7.1 - - - +
164B ALA* 3.6 31.2 - - + +
463C TRP* 3.8 29.6 - - + +
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 3.2 16.7 + - + -
66B LYS 3.1 16.8 + - - +
67B LEU* 3.7 7.6 - - + +
69B LYS* 1.3 75.1 - - - +
71B GLY* 1.3 64.4 + - - +
74B GLN* 2.7 57.2 + - - +
463C TRP* 3.9 24.7 - - + -
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B HIS* 3.7 16.5 - - - -
35B ILE* 4.2 6.0 - - - +
36B THR* 4.1 6.5 - - - +
55B PHE* 3.7 13.5 - - - -
67B LEU 2.7 20.7 + - - -
68B LEU 3.2 2.0 + - - -
70B ASP* 1.3 73.4 - - - +
72B LEU* 1.3 55.7 + - - +
74B GLN* 4.0 0.7 - - - +
75B TYR* 2.8 34.2 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.3 9.9 - - + -
55B PHE* 5.4 1.3 - - + -
56B LEU* 4.1 22.2 - - + -
68B LEU 3.0 20.3 + - - +
69B LYS* 3.8 4.9 - - - +
71B GLY* 1.3 75.4 - - - +
73B HIS* 1.3 57.4 + - - +
75B TYR* 3.3 6.8 + - + +
76B LYS* 2.8 30.5 + - - +
92B VAL* 3.8 33.2 - - + +
93B ALA* 5.3 1.6 - - - -
96B PHE* 3.5 37.2 - - + -
164B ALA* 6.6 0.2 - - + -
165B VAL* 5.1 2.7 - - + -
168B LEU* 3.8 28.0 - - + +
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 2.9 30.7 + - + +
70B ASP 4.2 1.8 - - - +
72B LEU* 1.3 73.2 - - - +
74B GLN* 1.3 59.3 + - - +
76B LYS* 3.1 6.6 + - + +
77B LYS* 2.9 37.0 + - + +
164B ALA* 4.4 9.0 - - + -
167B ASP* 4.1 7.0 + - + -
168B LEU* 3.6 45.2 - - + +
170B ARG* 5.5 0.8 + - - -
463C TRP* 3.5 64.5 - + + +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 4.0 3.2 + - - -
36B THR* 3.6 42.9 + - + +
70B ASP* 2.7 46.4 + - - +
73B HIS* 1.3 77.0 - - - +
75B TYR* 1.3 61.2 + - - +
77B LYS* 3.5 7.9 + - + +
78B LEU* 3.3 31.4 + - + +
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.7 32.3 - - + +
36B THR* 4.6 0.8 - - - +
40B ILE* 4.1 16.8 - - + -
45B PRO* 4.0 10.2 + - - +
48B VAL* 4.3 7.6 - - + +
49B GLU* 4.4 3.8 + - - -
52B VAL* 4.0 30.7 - - + -
71B GLY 2.8 20.5 + - - +
72B LEU* 3.7 6.3 - - + +
74B GLN* 1.3 77.2 - - - +
76B LYS* 1.3 63.8 + - - +
78B LEU* 3.1 6.1 + - - +
79B ILE* 3.0 56.9 + - + +
88B SER* 2.7 31.1 + - - -
89B VAL* 4.6 5.4 - - + -
92B VAL* 4.2 22.7 - - + -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU 2.8 17.0 + - - +
73B HIS* 3.1 7.2 + - + +
75B TYR* 1.3 77.8 - - + +
77B LYS* 1.3 69.4 + - + +
80B GLN* 2.8 58.8 + - + +
86B LEU* 6.0 0.7 - - - -
89B VAL* 3.7 38.4 - - + -
168B LEU* 3.7 40.2 + - + +
172B ASN* 4.6 8.3 - - - +
175B LEU* 4.1 19.1 - - - -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 3.9 17.8 + - - +
73B HIS* 2.9 22.0 + - + +
74B GLN* 3.8 9.2 - - + +
75B TYR 3.3 0.4 - - - -
76B LYS* 1.3 83.1 - - + +
78B LEU* 1.3 62.2 + - + +
80B GLN* 3.9 28.5 + - - +
445C GLN* 3.4 27.0 + - - +
449C TYR* 6.2 1.6 - - - -
466C GLU* 4.4 4.8 + - - -
484C HIS* 3.8 29.7 + - - +
487C ALA* 5.9 3.6 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE 3.8 12.1 - - - +
36B THR* 3.7 21.8 - - - +
37B ALA 3.3 27.8 - - - +
38B ARG* 4.1 21.5 - - + +
40B ILE* 4.2 6.5 - - + -
41B ARG* 3.4 61.0 + - + +
74B GLN* 3.3 18.6 + - + +
75B TYR* 3.1 6.2 + - - +
76B LYS 3.1 0.6 - - - -
77B LYS* 1.3 80.2 - - + +
79B ILE* 1.3 59.3 + - + +
80B GLN 3.6 0.4 - - - -
81B GLY 4.7 2.6 + - - -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.5 29.6 - - + +
41B ARG 5.0 2.9 - - - +
43B ALA 3.9 12.1 - - - +
45B PRO* 3.7 35.2 - - + -
75B TYR* 3.0 44.4 + - + +
76B LYS 3.8 0.4 - - - +
78B LEU* 1.3 77.9 - - + +
80B GLN* 1.3 60.7 + - - +
81B GLY 2.9 12.9 + - - -
82B SER* 3.6 6.9 + - - +
85B GLY* 3.2 18.3 - - - +
89B VAL* 3.6 27.1 - - + -
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 2.8 55.6 + - + +
77B LYS* 3.9 38.7 + - - +
78B LEU 3.6 0.2 - - - -
79B ILE* 1.3 77.0 - - + +
81B GLY* 1.3 64.1 + - - +
82B SER 3.2 1.3 - - - -
85B GLY 4.6 0.2 - - - -
86B LEU* 3.1 37.3 - - + +
89B VAL* 5.2 0.7 - - + -
172B ASN* 5.0 3.6 + - - -
223B ASN* 5.0 3.1 + - - -
484C HIS* 4.2 23.6 + - - +
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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
------------------------------------------------------------
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