Contacts of the helix formed by residues 48 - 62 (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 VAL 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO* 5.7 0.4 - - + -
34A PHE* 4.2 22.0 - - + -
35A ILE* 4.4 14.6 - - + -
40A ILE* 3.9 28.9 - - + -
43A ALA* 3.8 23.8 - - + -
44A THR 3.5 14.1 - - - +
45A PRO* 3.2 7.9 + - + +
47A THR* 1.3 82.0 - - - +
49A GLU* 1.3 57.5 + - - +
50A PRO* 3.3 3.4 - - - -
51A VAL* 2.8 34.6 + - - +
52A VAL* 3.4 8.5 + - + +
75A TYR* 4.6 5.8 - - + -
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Residues in contact with GLU 49 (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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45A PRO 3.1 15.2 + - - +
46A SER* 4.0 10.4 + - - +
48A VAL* 1.3 75.7 - - - +
50A PRO* 1.4 67.1 - - + +
52A VAL* 3.1 12.6 + - - +
53A PHE* 3.0 50.0 + - + -
75A TYR* 5.0 0.8 + - - -
88A SER* 3.5 24.4 + - - +
91A ALA* 3.3 27.2 - - - +
92A VAL* 4.0 6.1 - - + -
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Residues in contact with PRO 50 (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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8A PRO* 6.0 2.7 - - + -
12A ILE* 4.3 16.7 - - + +
46A SER 3.6 13.5 - - - +
47A THR* 4.2 5.2 - - - +
48A VAL 3.4 7.0 - - - +
49A GLU* 1.4 94.8 - - + +
51A VAL* 1.3 61.5 + - + +
53A PHE* 3.5 12.4 + - + +
54A LYS* 3.3 19.6 + - - +
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Residues in contact with VAL 51 (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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8A PRO* 3.5 39.7 - - + +
11A ALA* 4.4 2.7 - - + -
12A ILE* 4.5 9.4 - - + -
31A LEU* 3.8 25.1 - - + +
34A PHE* 3.6 33.9 - - + -
35A ILE* 3.7 13.2 - - + -
48A VAL 2.8 15.0 + - - +
50A PRO* 1.3 74.0 - - + +
52A VAL* 1.3 64.9 + - - +
54A LYS* 3.2 6.1 + - - +
55A PHE* 3.1 19.9 + - - +
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Residues in contact with VAL 52 (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* 3.6 35.7 - - + -
48A VAL* 3.9 10.5 - - + +
49A GLU* 3.1 13.4 + - - +
51A VAL* 1.3 73.9 - - - +
53A PHE* 1.3 60.9 + - - +
55A PHE* 3.1 8.6 + - - +
56A LEU* 2.9 39.3 + - + +
72A LEU* 4.6 5.2 - - + -
75A TYR* 4.4 23.6 - - + -
92A VAL* 3.6 33.0 - - + -
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Residues in contact with PHE 53 (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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49A GLU* 3.0 51.7 + - + -
50A PRO* 3.6 14.4 - - + +
52A VAL* 1.3 77.5 - - - +
54A LYS* 1.3 56.8 + - - +
56A LEU* 3.0 9.0 + - + +
57A GLU* 2.9 36.8 + - - +
91A ALA* 4.1 5.8 - - + -
92A VAL* 3.7 18.6 - - + -
95A LYS* 3.6 52.9 - - + +
99A LEU* 4.7 0.3 - - - +
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Residues in contact with LYS 54 (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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12A ILE* 4.6 21.5 - - + -
15A ALA* 4.9 3.4 - - + -
16A ASP* 3.3 31.8 + - - -
19A ILE* 4.8 3.9 - - - +
31A LEU* 3.5 20.0 - - + -
50A PRO 3.3 9.2 + - - +
51A VAL* 3.2 11.8 + - - +
53A PHE* 1.3 78.3 - - - +
55A PHE* 1.3 62.3 + - - +
57A GLU* 3.2 26.3 + - - +
58A ILE* 3.1 40.8 + - + +
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Residues in contact with PHE 55 (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* 3.4 37.5 - - + +
31A LEU* 3.7 15.9 - - + +
32A HIS* 4.1 34.8 - + + -
35A ILE* 3.9 22.2 - - + -
51A VAL 3.1 12.3 + - - +
52A VAL* 3.2 9.6 - - + +
54A LYS* 1.3 77.8 - - - +
56A LEU* 1.3 72.3 + - + +
59A GLY* 3.0 23.7 + - - -
67A LEU* 3.7 28.3 - - + -
68A LEU* 3.6 32.8 - - + +
71A GLY* 4.3 4.3 - - - -
72A LEU* 4.7 1.8 - - + -
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Residues in contact with LEU 56 (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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52A VAL* 2.9 21.6 + - + +
53A PHE* 3.0 10.1 + - + +
55A PHE* 1.3 92.6 - - + +
57A GLU* 1.3 67.5 + - - +
59A GLY 3.9 0.2 - - - -
60A VAL* 3.0 30.7 + - - +
68A LEU* 4.1 8.0 - - + +
72A LEU* 3.7 21.5 - - + -
92A VAL* 3.2 34.8 - - + +
95A LYS* 3.9 11.9 - - + -
96A PHE* 3.5 29.8 - - + +
99A LEU* 3.5 12.1 - - + -
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Residues in contact with GLU 57 (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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53A PHE* 2.9 21.3 + - - +
54A LYS* 3.5 35.7 + - - +
56A LEU* 1.3 77.6 - - - +
58A ILE* 1.3 64.8 + - + +
60A VAL* 3.5 2.4 + - - +
61A GLU* 3.2 29.7 + - + +
95A LYS* 4.2 17.6 + - - -
99A LEU* 3.5 23.1 - - + -
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Residues in contact with ILE 58 (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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15A ALA* 4.6 4.3 - - + -
19A ILE* 3.5 33.0 - - + -
24A LYS* 4.5 5.2 - - + +
28A LEU* 3.6 36.6 - - + +
31A LEU* 3.6 29.8 - - + -
54A LYS* 3.1 23.4 + - + +
57A GLU* 1.3 76.5 - - + +
59A GLY* 1.3 58.5 + - - +
61A GLU* 3.2 8.1 + - - +
62A LEU* 2.9 41.6 + - + +
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Residues in contact with GLY 59 (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* 3.4 21.9 - - - +
55A PHE 3.0 19.2 + - - -
57A GLU 3.3 0.2 - - - -
58A ILE* 1.3 76.6 - - - +
60A VAL* 1.3 56.9 + - - +
62A LEU 3.5 0.7 + - - -
63A LYS* 3.0 5.5 + - - -
64A LYS* 3.0 27.9 + - - -
68A LEU* 3.7 20.5 - - - +
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Residues in contact with VAL 60 (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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56A LEU 3.0 20.9 + - - +
57A GLU 3.9 3.6 - - - +
59A GLY* 1.3 75.0 - - - +
61A GLU* 1.3 68.7 + - - +
63A LYS* 3.0 10.9 + - - -
68A LEU* 4.1 4.3 - - + -
96A PHE* 3.7 34.1 - - + -
99A LEU* 4.1 19.3 - - + +
100A VAL* 3.8 15.5 - - + -
103A LYS* 3.9 31.9 - - + -
154A TRP* 3.4 14.9 - - - -
157A PHE* 4.4 5.8 - - + -
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Residues in contact with GLU 61 (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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57A GLU 3.2 16.6 + - - +
58A ILE* 3.2 10.0 + - + +
60A VAL* 1.3 80.2 - - - +
62A LEU* 1.3 66.9 + - + +
63A LYS* 3.4 1.2 + - - +
103A LYS* 3.1 39.5 + - - +
154A TRP* 4.2 10.2 - - - -
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Residues in contact with LEU 62 (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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24A LYS* 4.1 41.5 - - + +
25A GLN* 4.2 15.0 - - + +
28A LEU* 3.7 20.2 - - + -
58A ILE* 2.9 39.2 + - + +
59A GLY 4.1 1.3 - - - +
61A GLU* 1.3 80.3 - - + +
63A LYS* 1.3 70.0 + - - +
64A LYS* 3.1 30.6 + - + +
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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
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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