Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 1U4L
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLU 3.6 3.0 + - - -
55A LYS* 1.3 73.2 - - - +
57A TRP* 1.3 64.6 + - - +
59A ARG* 3.2 8.0 + - - +
60A GLU* 2.7 63.5 + - + +
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Residues in contact with TRP 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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15A ILE* 3.7 31.3 + - + -
16A ALA 5.2 2.8 + - - -
17A ARG* 3.9 4.0 - - - +
18A PRO* 3.4 47.3 - - + +
19A LEU* 3.8 11.9 - - + -
41A PHE* 3.6 32.3 - + - -
51A ALA* 4.1 3.4 - - + -
52A ASN 5.6 0.2 - - - -
55A LYS* 3.9 24.9 - - + +
56A LYS* 1.3 80.1 - - - +
58A VAL* 1.3 70.1 + - + +
60A GLU* 3.9 13.5 - - - +
61A TYR* 2.9 71.2 + + + -
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Residues in contact with VAL 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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39A VAL* 3.8 34.5 - - + -
41A PHE* 3.9 9.6 - - + -
51A ALA* 3.9 8.3 - - + -
52A ASN 3.0 31.6 - - - +
53A PRO* 4.0 4.9 - - + -
55A LYS* 3.4 16.8 - - + +
56A LYS 3.1 0.8 - - - -
57A TRP* 1.3 106.5 - - + +
59A ARG* 1.3 62.4 + - - +
61A TYR* 3.4 2.9 + - - +
62A ILE* 3.1 25.8 + - + +
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Residues in contact with ARG 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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53A PRO 4.8 7.8 + - - +
55A LYS 3.2 8.1 + - - +
56A LYS* 3.2 10.6 + - - +
58A VAL* 1.3 79.2 - - - +
60A GLU* 1.3 59.3 + - + +
62A ILE* 3.3 11.1 + - - +
63A ASN* 3.0 39.8 + - - +
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Residues in contact with GLU 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 LYS* 2.7 53.7 + - + +
57A TRP* 3.8 15.1 - - - +
58A VAL 3.3 0.2 - - - -
59A ARG* 1.3 75.4 - - + +
61A TYR* 1.3 70.4 + - + +
63A ASN* 3.2 13.8 + - - +
64A SER* 2.9 24.7 + - - -
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Residues in contact with TYR 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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18A PRO* 3.9 9.4 - - - +
19A LEU 2.5 30.4 + - - -
20A PRO* 4.5 0.2 - - - +
21A ARG* 3.5 35.5 + - + +
24A ILE* 3.4 30.1 - - + -
41A PHE* 3.8 11.9 - + + -
57A TRP* 2.9 57.3 + + + +
58A VAL 3.6 5.2 - - - +
60A GLU* 1.3 80.7 - - + +
62A ILE* 1.3 58.3 + - - +
64A SER* 3.2 7.1 + - - -
65A LEU* 2.8 37.0 + - + +
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Residues in contact with ILE 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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27A TYR* 3.7 35.4 - - + +
29A TYR* 3.0 41.3 - - + +
39A VAL* 3.8 18.6 - - + -
41A PHE* 4.4 8.3 - - + -
53A PRO* 6.0 0.9 - - + -
58A VAL* 3.1 18.8 + - + +
59A ARG* 3.5 11.7 - - - +
61A TYR* 1.3 75.2 - - - +
63A ASN* 1.3 71.8 + - - +
65A LEU* 3.2 8.1 + - - +
66A GLU* 3.0 28.4 + - + +
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Residues in contact with ASN 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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59A ARG* 3.0 27.0 + - - +
60A GLU* 3.5 13.1 - - - +
62A ILE* 1.3 82.3 - - - +
64A SER* 1.3 60.9 + - - +
66A GLU* 3.5 11.4 + - - +
67A MET* 3.4 25.1 + - + +
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Residues in contact with SER 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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21A ARG* 3.0 29.7 + - - -
60A GLU 2.9 13.7 + - - -
61A TYR* 3.4 9.2 - - - -
63A ASN* 1.3 76.0 - - - +
65A LEU* 1.3 60.5 + - - +
67A MET* 2.9 28.7 + - - +
68A SER* 3.3 9.9 + - - -
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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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21A ARG* 3.5 29.6 - - - +
24A ILE* 3.9 21.5 - - + +
25A LYS* 4.0 18.6 - - - +
26A GLU* 4.4 1.8 - - - +
27A TYR* 3.7 41.7 - - + -
41A PHE* 3.9 16.4 - - + -
61A TYR* 2.8 25.4 + - + +
62A ILE 3.7 3.8 - - - +
64A SER* 1.3 73.0 + - - +
66A GLU* 1.3 61.3 + - - +
67A MET 3.1 1.3 + - - -
68A SER* 3.6 18.7 + - - +
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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