Contacts of the helix formed by residues 56 - 65 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B VAL 3.4 2.1 + - - +
55B GLY* 1.3 68.5 - - - -
57B GLU* 1.3 63.9 + - - +
58B ALA 2.9 4.9 - - - -
59B GLN* 2.9 26.4 + - + +
60B SER* 3.1 19.2 + - - -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 3.6 2.0 + - - -
54B VAL 3.3 20.6 + - - +
56B ASP* 1.3 80.8 + - - +
58B ALA* 1.3 47.2 - - - +
60B SER* 4.4 3.1 - - - +
61B LYS* 4.4 0.8 + - - +
149D THR* 5.2 8.2 + - + +
166D TYR* 2.1 36.5 + - - -
167D GLU* 2.7 24.5 - - - +
289D ILE* 5.5 0.2 - - - -
292D ASP* 4.7 16.8 - - - +
127M GLU* 5.2 2.9 - - - +
128M GLU* 2.7 35.1 - - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.9 2.2 - - + +
36B GLY 4.5 0.9 - - - +
53B TYR* 3.6 31.9 - - + +
54B VAL 4.0 2.0 - - - +
55B GLY 3.5 12.5 + - - +
56B ASP 2.9 0.8 - - - -
57B GLU* 1.3 68.8 - - - +
59B GLN* 1.3 64.7 + - - +
62B ARG* 3.3 16.8 + - - +
65B LEU* 4.5 1.8 - - + -
67B LEU* 3.7 23.0 - - + +
166D TYR* 1.5 43.7 + - + +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER 5.1 6.4 - - - +
34B ILE* 4.4 12.3 - - + +
55B GLY 3.5 4.3 + - - +
56B ASP* 2.9 22.9 + - + +
58B ALA* 1.3 79.2 - - - +
60B SER* 1.3 58.2 + - - +
61B LYS 3.1 0.2 - - - -
62B ARG* 2.8 70.5 + - - +
67B LEU* 5.4 0.2 - - - +
70B PRO* 5.8 3.1 - - - +
203B THR* 3.4 9.4 - - - +
207B GLU* 4.9 12.8 - - + +
288D ASP* 3.8 22.2 - - + +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP 3.1 14.8 + - - -
57B GLU 5.1 0.4 - - - -
58B ALA 3.3 0.4 - - - +
59B GLN* 1.3 73.2 - - - +
61B LYS* 1.3 46.9 - - - +
204B ALA* 3.6 2.1 - - - +
286D ASP* 3.8 4.7 - - - -
288D ASP* 1.6 62.8 + - - +
289D ILE* 1.2 100.3 - - - +
291D LYS* 4.8 0.3 - - - +
292D ASP* 4.6 2.7 - - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU 4.4 0.2 + - - -
59B GLN 3.1 0.4 - - - -
60B SER* 1.3 74.4 - - - +
62B ARG* 1.4 57.6 + - - +
63B GLY 3.2 3.1 - - - -
64B ILE* 2.8 24.6 + - + -
65B LEU 2.9 8.7 + - - -
149D THR* 1.5 46.2 - - - +
165D ILE 3.1 2.5 - - - -
166D TYR* 0.8 329.2 - - + +
286D ASP* 3.8 3.5 + - - -
289D ILE* 2.9 28.4 - - + +
293D LEU* 5.2 0.6 - - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.8 4.6 - - - +
58B ALA 3.3 14.0 + - - +
59B GLN* 2.8 53.1 + - - +
61B LYS* 1.4 72.9 - - - +
63B GLY* 1.3 64.4 + - - +
65B LEU* 2.9 26.4 - - - +
67B LEU* 3.9 28.7 - - + +
69B TYR* 3.9 14.6 + - - -
70B PRO* 4.9 13.5 - - - +
77B THR* 5.7 1.6 + - - -
78B ASN* 4.4 25.5 - - - +
203B THR* 4.2 13.5 - - + -
166D TYR* 4.5 0.7 - - - -
286D ASP* 3.5 1.0 + - - +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS 3.2 0.6 - - - -
62B ARG* 1.3 85.0 - - - +
64B ILE* 1.3 60.5 + - - +
65B LEU 3.6 0.9 + - - +
286D ASP* 3.2 13.4 + - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO 4.1 8.7 - - - +
61B LYS* 2.8 27.4 + - + +
63B GLY* 1.3 72.7 - - - +
65B LEU* 1.4 61.0 + - + +
166D TYR* 3.0 28.3 - - + +
169D TYR* 5.6 2.1 - - - +
171D LEU* 1.5 92.0 - - + -
172D PRO* 5.9 0.9 - - + -
173D HIS* 3.5 27.4 - - + +
286D ASP* 4.8 4.4 + - + +
289D ILE* 4.1 0.4 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 3.9 16.4 - - - +
37B ARG 4.2 3.1 - - - +
38B PRO* 3.6 37.5 - - + -
53B TYR* 3.8 11.9 - - + -
58B ALA* 4.4 2.5 - - + +
61B LYS 2.9 6.3 + - - +
62B ARG* 2.9 18.7 + - - +
63B GLY 3.4 0.9 - - - +
64B ILE* 1.4 84.3 - - + +
66B THR* 1.3 66.4 + - - +
67B LEU* 3.8 5.3 + - + +
166D TYR* 2.3 64.8 - - + +
169D TYR* 3.8 6.5 - - + -
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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