Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 3LUE
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 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 VAL 3.4 1.8 + - - +
55A GLY* 1.3 69.0 - - - -
57A GLU* 1.3 63.8 + - - +
58A ALA 2.9 4.9 - - - -
59A GLN* 2.9 26.7 + - + +
60A SER* 3.1 19.6 + - - -
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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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50A LYS* 3.6 1.9 + - - -
54A VAL 3.3 21.4 + - - +
56A ASP* 1.3 81.0 + - - +
58A ALA* 1.3 48.9 - - - +
60A SER* 4.4 2.2 - - - -
61A LYS* 4.4 0.3 + - - -
149C THR* 5.2 7.6 + - + +
166C TYR* 2.1 37.0 + - - -
167C GLU* 2.7 24.3 - - - +
289C ILE* 5.5 0.2 - - - -
292C ASP* 4.7 17.3 - - - +
127K GLU* 5.2 2.9 - - - +
128K GLU* 2.7 35.3 - - - +
136K MET* 6.2 0.2 - - - -
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Residues in contact with ALA 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 ILE* 4.9 2.5 - - + +
36A GLY 4.5 0.7 - - - +
53A TYR* 3.6 31.9 - - + +
54A VAL* 4.0 2.2 - - - +
55A GLY 3.5 11.6 + - - +
56A ASP 2.9 1.0 - - - -
57A GLU* 1.3 67.4 - - - +
59A GLN* 1.3 65.6 + - - +
62A ARG* 3.3 16.8 + - - +
65A LEU* 4.5 2.0 - - + -
67A LEU* 3.7 22.0 - - + +
166C TYR* 1.5 43.4 + - + +
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Residues in contact with GLN 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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33A SER 5.1 6.8 - - - +
34A ILE* 4.4 12.7 - - + +
55A GLY 3.5 4.7 + - - +
56A ASP* 2.9 22.6 + - + +
58A ALA* 1.3 80.0 - - - +
60A SER* 1.3 58.0 + - - +
61A LYS 2.9 0.6 + - - -
62A ARG* 2.8 70.4 + - - +
70A PRO* 5.8 2.8 - - - +
203A THR* 3.4 9.4 - - - +
207A GLU* 4.9 13.2 - - + +
288C ASP* 3.8 22.9 - - + +
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Residues in contact with SER 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 ASP* 3.1 15.7 + - - +
57A GLU 5.1 0.2 - - - -
58A ALA 3.3 0.2 - - - -
59A GLN* 1.3 73.2 - - - +
61A LYS* 1.3 46.2 - - - +
204A ALA* 3.6 2.1 - - - +
166C TYR* 4.2 0.2 - - - -
286C ASP* 3.8 5.6 - - - -
288C ASP* 1.6 64.0 + - - +
289C ILE* 1.2 99.3 - - - +
291C LYS* 4.8 0.2 - - - +
292C ASP* 4.6 3.3 + - - -
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Residues in contact with LYS 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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59A GLN 3.1 0.4 - - - -
60A SER* 1.3 73.6 - - - +
62A ARG* 1.4 57.3 + - - +
63A GLY 3.2 3.1 - - - -
64A ILE* 2.8 24.4 + - + -
65A LEU 2.9 8.3 + - - -
149C THR* 1.5 46.2 - - - +
165C ILE 3.1 2.2 - - - -
166C TYR* 0.8 330.2 - - + +
286C ASP* 3.8 4.5 + - - -
289C ILE* 2.9 28.9 - - + +
293C LEU* 5.2 0.9 - - - +
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Residues in contact with ARG 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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34A ILE* 4.8 4.2 - - - +
58A ALA 3.3 12.9 + - - +
59A GLN* 2.8 51.6 + - - +
61A LYS* 1.4 72.1 - - - +
63A GLY* 1.3 63.4 + - - +
65A LEU* 2.9 27.0 - - - +
67A LEU* 3.9 30.3 - - + +
69A TYR* 3.9 14.8 + - - -
70A PRO* 4.9 13.7 - - - +
77A THR* 5.7 1.6 + - - -
78A ASN* 4.4 25.3 - - - +
81A ASP* 5.4 0.2 - - - -
203A THR* 4.2 13.2 - - + -
166C TYR* 4.5 0.4 - - - -
286C ASP* 3.5 1.0 + - - +
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Residues in contact with GLY 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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61A LYS 3.2 0.6 - - - -
62A ARG* 1.3 84.9 - - - +
64A ILE* 1.3 59.0 + - - +
65A LEU 3.6 0.7 + - - +
203A THR* 4.9 0.2 - - - +
286C ASP* 3.2 14.5 + - - -
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Residues in contact with ILE 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 PRO 4.1 9.4 - - - +
61A LYS* 2.8 28.0 + - + +
63A GLY* 1.3 73.8 - - - +
65A LEU* 1.4 60.1 + - + +
166C TYR* 3.0 27.1 - - + +
169C TYR* 5.6 1.9 - - - +
171C LEU* 1.5 92.0 - - + -
172C PRO* 5.9 0.9 - - + -
173C HIS* 3.5 26.9 - - + +
286C ASP* 4.8 4.6 + - + +
289C ILE* 4.1 0.7 - - + -
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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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36A GLY* 3.9 16.2 - - - +
37A ARG 4.2 2.9 - - - +
38A PRO* 3.6 38.4 - - + -
53A TYR* 3.8 11.9 - - + -
58A ALA* 4.4 2.7 - - - +
61A LYS 2.9 6.3 + - - +
62A ARG* 2.9 18.9 + - - +
63A GLY 3.4 0.9 - - - +
64A ILE* 1.4 83.9 - - + +
66A THR* 1.3 65.3 + - - +
67A LEU* 3.8 4.3 + - + +
166C TYR* 2.3 64.6 - - + +
169C TYR* 3.8 5.6 - - + -
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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