Contacts of the helix formed by residues 49 - 70 (chain A) in PDB entry 4UAL
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 ASP 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ALA 4.8 4.5 - - - +
46A LEU* 2.9 15.0 + - - +
48A ARG* 1.3 83.1 - - + +
50A LYS* 1.3 67.4 + - - +
51A TYR* 2.8 38.1 + - - +
52A VAL* 3.1 17.9 + - + +
53A ALA* 2.9 23.7 + - - +
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Residues in contact with LYS 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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48A ARG 3.5 3.6 + - - -
49A ASP* 1.3 75.4 + - - +
51A TYR* 1.3 87.4 + - + +
53A ALA* 3.5 7.0 + - - +
54A GLU* 3.1 54.9 + - + +
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP* 2.8 18.3 + - - +
50A LYS* 1.3 100.4 - - + +
52A VAL* 1.3 67.5 + - + +
54A GLU* 3.8 15.0 - - - +
55A PHE* 3.1 22.0 + - - +
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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
----------------------------------------------------------
41A CYS* 3.6 46.4 - - + +
46A LEU* 3.1 39.3 - - + +
47A ARG* 3.9 2.2 - - - -
49A ASP* 3.1 15.1 + - + +
51A TYR* 1.3 75.8 - - + +
53A ALA* 1.3 57.6 + - - +
55A PHE* 3.1 7.3 + - - +
56A LEU* 2.9 29.6 + - + +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG 3.5 16.7 + - - +
48A ARG 5.2 0.9 - - - +
49A ASP 2.9 17.7 + - - +
50A LYS* 3.6 7.9 - - - +
52A VAL* 1.3 75.1 - - - +
54A GLU* 1.3 63.5 + - + +
56A LEU* 3.2 10.6 + - - +
57A GLU* 3.0 22.5 + - - +
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Residues in contact with GLU 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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50A LYS* 3.1 48.4 + - + +
51A TYR* 3.8 15.4 - - - +
52A VAL 3.2 0.2 - - - -
53A ALA* 1.3 76.6 - - + +
55A PHE* 1.3 62.8 + - - +
57A GLU* 3.4 14.7 + - - +
58A TRP* 3.0 24.3 + - - +
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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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34A LEU* 4.6 12.6 - - + -
37A LEU* 3.8 28.7 - - + -
38A TYR* 4.5 14.4 - + - -
41A CYS* 4.1 30.1 - - + -
51A TYR 3.1 14.3 + - - +
52A VAL* 3.1 10.5 + - - +
54A GLU* 1.3 78.3 - - - +
56A LEU* 1.3 59.9 + - - +
58A TRP* 3.2 33.0 + + - +
59A ALA* 2.8 44.1 + - + +
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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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38A TYR* 3.5 54.4 + - + +
41A CYS* 3.8 21.3 - - + +
42A SER* 3.9 9.2 - - - +
47A ARG* 3.7 32.5 - - + -
52A VAL 2.9 17.6 + - - +
53A ALA* 3.2 10.1 + - - +
55A PHE* 1.3 75.9 - - + +
57A GLU* 1.3 63.5 + - - +
60A LYS* 3.0 28.3 + - - +
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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 ALA 3.0 13.1 + - - +
54A GLU* 3.6 15.9 - - - +
56A LEU* 1.3 77.1 - - - +
58A TRP* 1.3 64.6 + - - +
60A LYS* 3.7 7.2 - - - +
61A PRO* 3.4 18.4 - - - +
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Residues in contact with TRP 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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34A LEU* 6.0 2.7 - - + -
54A GLU 3.0 17.6 + - - +
55A PHE* 3.6 30.5 - + - +
57A GLU* 1.3 80.3 - - - +
59A ALA* 1.3 84.3 + - + +
60A LYS 3.6 0.2 + - - -
61A PRO* 3.6 10.0 - - - +
62A PHE* 5.4 0.9 + - - +
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Residues in contact with ALA 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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34A LEU* 5.0 4.0 - - + -
38A TYR* 3.9 15.0 - - + -
55A PHE* 2.8 31.7 + - + +
58A TRP* 1.3 95.1 - - + +
60A LYS* 1.3 59.6 + - - +
61A PRO 3.4 1.2 - - - -
62A PHE* 3.5 6.5 + - - +
63A THR* 2.8 43.4 + - - +
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Residues in contact with LYS 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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38A TYR* 3.4 22.9 - - - +
56A LEU 3.0 18.4 + - - +
57A GLU* 3.7 8.1 - - - +
58A TRP 3.3 0.2 - - - -
59A ALA* 1.3 76.9 - - - +
61A PRO* 1.3 73.6 - - + +
63A THR 4.6 0.2 - - - +
64A GLN* 2.7 63.6 + - - +
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Residues in contact with PRO 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 3.4 11.9 - - - +
58A TRP 3.6 11.2 - - - +
59A ALA 3.7 0.4 - - - -
60A LYS* 1.3 99.6 - - + +
62A PHE* 1.3 60.9 + - - +
64A GLN* 4.0 4.8 - - + +
65A LEU* 3.1 26.8 + - - +
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Residues in contact with PHE 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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31A LEU* 3.9 17.0 - - + -
34A LEU* 3.7 27.6 - - + -
58A TRP 5.4 0.6 + - - +
59A ALA* 3.5 7.2 + - - +
60A LYS 3.3 0.2 - - - -
61A PRO* 1.3 78.7 - - - +
63A THR* 1.3 61.2 + - - +
65A LEU* 3.2 14.7 + - + +
66A VAL* 2.9 52.5 + - + +
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Residues in contact with THR 63 (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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34A LEU* 3.6 24.8 - - + +
35A VAL* 4.4 17.0 - - + -
38A TYR* 3.7 36.0 - - + -
59A ALA* 2.8 27.9 + - - +
60A LYS 4.1 0.9 - - - -
62A PHE* 1.3 75.3 - - - +
64A GLN* 1.3 63.8 + - - +
66A VAL* 3.2 3.9 + - - +
67A LYS* 3.0 42.8 + - - +
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Residues in contact with GLN 64 (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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38A TYR* 4.9 2.9 + - - +
60A LYS* 2.7 64.9 + - + +
61A PRO* 4.0 4.2 - - + +
63A THR* 1.3 74.5 - - - +
65A LEU* 1.3 56.2 + - - +
67A LYS* 3.8 19.2 + - - +
68A GLU* 2.9 54.9 + - + +
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Residues in contact with LEU 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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61A PRO 3.1 19.0 + - - +
62A PHE* 3.2 18.8 + - + +
64A GLN* 1.3 75.3 - - - +
66A VAL* 1.3 65.2 + - + +
68A GLU* 3.3 16.3 + - - +
69A MET* 2.9 50.6 + - + +
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Residues in contact with VAL 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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31A LEU* 4.2 21.3 - - + -
34A LEU* 5.3 1.6 - - + -
35A VAL* 4.3 15.5 - - + -
62A PHE* 2.9 53.4 + - + +
63A THR* 3.7 6.3 - - - +
65A LEU* 1.3 75.8 - - + +
67A LYS* 1.3 58.7 + - - +
69A MET* 3.9 2.6 - - - -
70A GLN* 2.9 61.0 + - + +
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Residues in contact with LYS 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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35A VAL* 4.3 29.4 - - + -
38A TYR* 3.7 23.0 - - - -
39A THR* 5.3 4.9 + - - +
63A THR* 3.0 41.5 + - - +
64A GLN* 3.8 15.7 + - - +
66A VAL* 1.3 77.5 - - - +
68A GLU* 1.3 56.2 + - + +
70A GLN* 3.8 8.0 + - - +
72A HIS* 2.6 32.8 + - - -
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Residues in contact with GLU 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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64A GLN* 2.9 47.7 + - - +
65A LEU* 3.7 22.8 - - - +
67A LYS* 1.3 80.1 - - + +
69A MET* 1.3 62.6 + - + +
70A GLN 3.7 0.2 - - - +
72A HIS* 3.1 21.3 - - - -
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Residues in contact with MET 69 (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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65A LEU* 2.9 39.0 + - + +
66A VAL* 4.2 3.1 - - - +
68A GLU* 1.3 75.4 - - + +
70A GLN* 1.3 71.1 + - + +
71A LEU* 5.4 2.1 - - - +
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Residues in contact with GLN 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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28A GLU* 4.8 7.7 + - - +
31A LEU* 4.1 22.1 - - - +
32A ASP* 4.9 7.1 + - - +
35A VAL* 4.8 7.8 - - - +
66A VAL* 2.9 42.3 + - + +
67A LYS* 3.8 6.9 + - - +
68A GLU 3.3 1.0 - - - -
69A MET* 1.3 84.5 - - + +
71A LEU* 1.3 64.8 + - - +
72A HIS* 3.0 22.7 + - - +
75A ASP* 4.2 1.9 - - - +
143A PHE* 6.5 0.4 - - + -
402A THR* 4.3 23.9 + - + +
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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