Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 3UC5
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A MET 4.2 0.6 + - - -
45A PHE* 1.3 75.5 - - - +
47A LEU* 1.3 65.6 + - - +
48A ASP* 3.1 13.5 + - - +
49A GLU* 2.8 47.0 + - - +
50A ARG* 3.0 18.1 + - - +
155A ARG* 5.4 0.2 - - - +
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Residues in contact with LEU 47 (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 30.1 - - + -
37A VAL* 4.5 25.6 - - + +
46A ASP* 1.3 73.9 - - - +
48A ASP* 1.3 64.6 + - - +
50A ARG* 3.1 9.8 + - - +
51A ILE* 2.9 35.5 + - + +
68A VAL* 3.6 46.7 - - + -
70A HIS* 5.7 2.2 - - + -
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Residues in contact with ASP 48 (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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46A ASP* 3.1 10.4 + - - +
47A LEU* 1.3 83.0 + - - +
49A GLU* 1.3 62.3 + - - +
51A ILE* 3.7 14.5 - - - +
52A ALA* 3.0 25.1 + - - +
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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 PHE* 3.4 34.7 - - + -
46A ASP* 2.8 52.6 + - - +
48A ASP* 1.3 71.7 - - + +
50A ARG* 1.3 63.2 + - - +
52A ALA* 3.3 5.0 + - - +
53A MET* 3.0 32.1 + - + +
151A ARG* 5.2 14.9 - - - +
155A ARG* 4.0 16.0 + - - -
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Residues in contact with ARG 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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9A SER* 3.0 42.5 + - - +
10A PHE 3.6 15.3 - - - +
11A ASP* 3.5 24.7 + - - +
35A ILE* 3.8 20.8 - - + +
37A VAL* 4.0 33.9 - - - +
38A ASN 5.0 1.2 - - - +
43A GLY* 4.0 13.9 - - - -
45A PHE* 2.8 31.3 + - + +
46A ASP 3.0 17.6 + - - +
47A LEU* 3.4 9.4 - - - +
49A GLU* 1.3 76.1 - - - +
51A ILE* 1.3 63.2 + - - +
53A MET* 3.3 11.7 + - + +
54A VAL* 3.2 26.9 + - - +
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Residues in contact with ILE 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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35A ILE* 3.6 21.3 - - + -
47A LEU* 2.9 26.7 + - + +
48A ASP* 3.7 15.0 - - - +
50A ARG* 1.3 76.1 - - - +
52A ALA* 1.3 62.6 - - - +
54A VAL* 3.3 3.5 + - - +
55A LYS* 3.0 51.9 + - + +
66A VAL* 4.3 10.3 - - + +
67A GLN* 5.5 0.4 - - - -
68A VAL* 3.5 31.6 - - + +
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Residues in contact with ALA 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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48A ASP 3.0 18.3 + - - +
49A GLU* 3.8 5.4 - - - +
50A ARG 3.3 0.2 - - - -
51A ILE* 1.3 79.0 - - - +
53A MET* 1.3 57.5 + - - +
55A LYS* 3.8 6.6 - - - +
56A GLU* 2.9 40.8 + - - +
151A ARG* 3.7 21.3 - - - +
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Residues in contact with MET 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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10A PHE 4.9 0.4 - - - +
12A PRO* 3.7 17.7 - - + -
13A VAL* 4.1 12.8 - - + +
45A PHE* 3.6 38.4 - - + -
49A GLU 3.0 22.1 + - - +
50A ARG* 3.8 14.4 - - - +
52A ALA* 1.3 75.2 - - - +
54A VAL* 1.3 60.8 + - - +
56A GLU* 3.9 2.2 - - - +
57A SER* 2.5 34.5 + - - -
147A PRO* 4.4 2.6 - - - +
148A VAL* 3.9 28.5 - - + -
151A ARG* 3.5 41.3 - - - +
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Residues in contact with VAL 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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10A PHE* 4.3 17.9 - - + +
13A VAL* 3.9 28.5 - - + -
21A PHE* 4.0 20.6 - - + -
33A VAL* 4.1 14.4 - - + -
35A ILE* 4.5 7.0 - - + -
50A ARG 3.2 14.1 + - - +
51A ILE 3.8 5.6 - - - +
53A MET* 1.3 74.6 - - - +
55A LYS* 1.3 63.4 + - - +
57A SER* 3.1 9.3 + - - -
58A THR* 2.8 25.8 + - + +
66A VAL* 3.4 24.9 - - + -
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Residues in contact with LYS 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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51A ILE* 3.0 44.0 + - + +
52A ALA* 3.8 7.0 - - - +
54A VAL* 1.3 75.2 - - - +
56A GLU* 1.3 63.0 + - + +
58A THR* 3.1 19.0 + - - -
59A THR* 3.5 14.4 + - - +
66A VAL* 3.7 31.8 + - + +
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Residues in contact with GLU 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 ALA* 2.9 21.9 + - - +
53A MET 4.0 0.2 - - - +
55A LYS* 1.3 76.7 - - + +
57A SER* 1.3 59.4 + - - +
58A THR 3.6 0.3 + - - -
59A THR* 3.9 19.0 + - - +
147A PRO* 3.4 22.8 - - + +
150A ARG* 3.2 19.2 + - - -
151A ARG* 2.8 44.5 + - - -
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Residues in contact with SER 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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13A VAL* 4.2 3.3 - - - +
18A VAL* 4.0 15.3 - - - +
53A MET 2.5 23.6 + - - -
54A VAL* 3.8 6.5 - - - -
55A LYS 3.1 0.8 - - - -
56A GLU* 1.3 76.6 - - - +
58A THR* 1.3 62.3 + - - +
59A THR* 3.7 1.1 - - - -
60A HIS* 3.3 19.0 - - - -
145A PRO* 3.4 36.6 - - - +
147A PRO* 3.7 12.3 - - - +
148A VAL* 4.6 0.3 - - - +
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Residues in contact with THR 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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18A VAL* 4.9 3.6 - - + -
21A PHE* 3.7 32.8 - - + -
54A VAL* 2.8 26.4 + - + +
55A LYS* 3.1 9.0 + - - -
57A SER* 1.3 87.7 - - - +
59A THR* 1.3 61.0 + - - +
60A HIS* 3.0 12.1 - - - -
61A LEU* 3.0 31.3 + - + +
64A LEU* 3.6 26.6 - - + +
66A VAL* 4.7 0.2 - - - +
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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