Contacts of the helix formed by residues 48 - 62 (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 VAL 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 5.4 3.4 - - + -
34B PHE* 4.1 19.3 - - + -
35B ILE* 4.7 7.9 - - + -
39B ARG* 5.7 1.1 - - - +
40B ILE* 4.1 33.9 - - + -
43B ALA* 3.6 31.2 - - + -
44B THR 3.7 6.5 - - - +
45B PRO* 3.1 7.7 + - + +
47B THR* 1.3 84.3 - - - +
49B GLU* 1.3 56.5 + - - +
50B PRO* 3.2 3.4 - - - -
51B VAL* 2.8 33.9 + - - +
52B VAL* 3.5 3.2 + - + -
75B TYR* 4.3 12.3 - - + -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO 3.0 16.1 + - - +
46B SER* 3.9 12.1 + - - +
48B VAL* 1.3 76.0 - - - +
50B PRO* 1.3 68.0 - - + +
52B VAL* 3.1 7.7 + - - +
53B PHE* 3.0 49.8 + - + -
75B TYR* 4.4 6.6 + - - -
88B SER* 3.4 26.7 + - - +
91B ALA* 3.2 28.5 - - - +
92B VAL* 4.0 3.4 - - + -
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 6.3 1.3 - - + -
12B ILE* 4.0 15.9 - - + +
46B SER 3.6 14.4 - - - +
47B THR* 4.0 6.3 - - - +
48B VAL 3.3 7.4 - - - +
49B GLU* 1.3 94.7 - - + +
51B VAL* 1.3 61.7 + - + +
53B PHE* 3.3 13.6 + - + +
54B LYS* 3.0 21.5 + - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.9 31.6 - - + +
11B ALA* 4.7 1.3 - - + -
12B ILE* 4.1 11.0 - - + -
31B LEU* 3.6 26.2 - - + +
34B PHE* 3.4 43.1 - - + -
35B ILE* 3.5 11.2 - - + -
48B VAL 2.8 16.7 + - - +
50B PRO* 1.3 74.1 - - + +
52B VAL* 1.3 57.1 + - - +
54B LYS* 3.1 4.5 + - - +
55B PHE* 2.8 26.9 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.6 34.5 - - + -
48B VAL 4.1 7.9 - - - +
49B GLU* 3.1 8.2 + - - +
51B VAL* 1.3 73.5 - - - +
53B PHE* 1.3 61.1 + - - +
55B PHE* 3.1 8.4 + - + +
56B LEU* 2.8 36.2 + - + +
72B LEU* 4.3 11.9 - - + -
75B TYR* 4.0 31.2 - - + -
92B VAL* 3.5 31.4 - - + -
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.0 38.6 + - + -
50B PRO* 3.4 15.5 - - + +
52B VAL* 1.3 76.9 - - - +
54B LYS* 1.3 57.7 + - - +
56B LEU* 3.1 9.0 + - + +
57B GLU* 2.9 37.8 + - - +
91B ALA* 4.0 6.3 - - + -
92B VAL* 3.6 26.2 - - + -
95B LYS* 3.6 52.2 - - + -
99B LEU* 4.6 0.3 - - - +
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Residues in contact with LYS 54 (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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12B ILE* 4.0 27.1 - - + +
15B ALA* 4.5 6.5 - - + -
16B ASP* 2.8 35.5 + - - +
19B ILE* 4.9 4.7 - - - +
31B LEU* 3.4 18.6 - - + -
50B PRO 3.0 13.6 + - - +
51B VAL* 3.1 11.9 + - - +
53B PHE* 1.3 75.9 - - - +
55B PHE* 1.3 62.9 + - - +
57B GLU* 3.2 21.3 + - - +
58B ILE* 3.1 42.6 + - + +
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Residues in contact with PHE 55 (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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28B LEU* 3.4 34.2 - - + +
31B LEU* 3.6 15.6 - - + +
32B HIS* 3.6 44.2 - - + -
35B ILE* 3.4 18.6 - - + -
51B VAL 2.8 12.9 + - - +
52B VAL* 3.3 13.2 - - + +
54B LYS* 1.3 76.2 - - - +
56B LEU* 1.3 64.8 + - + +
59B GLY* 3.0 23.2 + - - -
67B LEU* 3.6 29.6 - - + -
68B LEU* 3.9 21.6 - - + +
71B GLY* 3.7 18.6 - - - -
72B LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 56 (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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52B VAL* 2.8 32.8 + - + +
53B PHE* 3.1 7.2 + - - +
55B PHE* 1.3 79.0 - - + +
57B GLU* 1.3 59.5 + - - +
59B GLY 3.7 0.2 - - - -
60B VAL* 2.9 36.4 + - - +
68B LEU* 3.7 20.4 - - + -
72B LEU* 4.1 18.6 - - + -
92B VAL* 3.4 26.5 - - + +
95B LYS* 4.0 13.0 - - + -
96B PHE* 3.9 32.8 - - + +
99B LEU* 3.5 13.5 - - + -
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Residues in contact with GLU 57 (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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53B PHE* 2.9 25.3 + - - +
54B LYS* 3.2 25.3 + - + +
56B LEU* 1.3 76.8 - - - +
58B ILE* 1.3 64.1 + - + +
60B VAL* 3.4 2.6 + - - +
61B GLU* 3.2 28.8 + - + +
95B LYS* 3.8 21.2 + - - -
99B LEU* 3.5 22.2 - - + -
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 4.5 5.2 - - + -
19B ILE* 3.7 30.5 - - + -
24B LYS* 4.4 4.5 - - + +
27B ALA* 4.7 0.2 - - + -
28B LEU* 3.4 41.1 - - + +
31B LEU* 3.6 29.8 - - + -
54B LYS* 3.1 24.5 + - - +
57B GLU* 1.3 73.4 - - + +
59B GLY* 1.3 65.2 + - - +
61B GLU* 3.1 7.8 + - + +
62B LEU* 3.0 35.9 + - + +
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Residues in contact with GLY 59 (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 19.0 - - - +
55B PHE 3.0 18.7 + - - -
56B LEU 3.7 1.1 - - - -
58B ILE* 1.3 77.0 - - - +
60B VAL* 1.3 56.3 + - - +
62B LEU 3.5 0.5 + - - -
63B LYS* 3.0 22.2 + - - -
64B LYS* 3.0 12.4 + - - -
68B LEU* 3.6 21.9 - - - +
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Residues in contact with VAL 60 (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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56B LEU 2.9 19.7 + - - +
57B GLU 3.8 4.5 - - - +
59B GLY* 1.3 75.6 - - - +
61B GLU* 1.3 69.8 + - - +
63B LYS* 3.0 13.0 + - - +
68B LEU* 4.3 1.3 - - + -
96B PHE* 3.9 28.9 - - + -
99B LEU* 3.9 29.6 - - + +
100B VAL* 4.4 6.5 - - - +
103B LYS* 3.5 30.3 - - + -
154B TRP* 3.7 11.3 - - - -
157B PHE* 4.3 14.8 - - + -
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Residues in contact with GLU 61 (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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24B LYS* 6.0 4.5 - - - +
57B GLU 3.2 16.8 - - - +
58B ILE* 3.1 8.9 + - - +
60B VAL* 1.3 78.8 - - - +
62B LEU* 1.3 67.4 + - + +
63B LYS* 3.2 1.4 + - - +
103B LYS* 3.4 40.0 + - - +
154B TRP* 4.4 12.6 - - - -
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Residues in contact with LEU 62 (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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24B LYS* 4.0 46.9 - - + +
25B GLN* 4.1 9.6 - - + +
28B LEU* 3.9 14.6 - - + -
58B ILE* 3.0 34.9 + - + +
59B GLY 4.2 1.1 - - - +
61B GLU* 1.3 80.2 - - + +
63B LYS* 1.3 69.5 + - - +
64B LYS* 3.1 33.2 + - + +
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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