Contacts of the helix formed by residues 53 - 67 (chain B) in PDB entry 2LDX
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ASP* 2.6 33.2 - - - +
52B ALA* 1.3 78.9 + - - +
54B THR* 1.3 53.6 + - - +
55B ASP* 2.5 23.2 + - + +
56B LYS* 3.1 19.6 + - + +
57B LEU* 3.5 9.4 + - - -
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Residues in contact with THR 54 (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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51B ASP 5.1 1.1 - - - -
52B ALA* 3.1 4.2 - - - +
53B ASP* 1.3 74.1 - - - +
55B ASP* 1.3 91.1 + - - +
57B LEU* 4.1 2.0 - - - +
58B ARG* 3.3 29.6 + - - +
78B PHE* 3.8 16.3 - - - -
80B LYS* 3.7 40.6 - - - +
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Residues in contact with ASP 55 (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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53B ASP* 2.5 9.5 + - + +
54B THR* 1.3 95.9 - - - +
56B LYS* 1.3 67.6 + - - +
57B LEU 3.0 0.3 + - - -
58B ARG* 3.2 8.8 + - - +
59B GLY* 3.4 7.1 + - - -
243D MET* 4.3 19.0 - - + +
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Residues in contact with LYS 56 (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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27B VAL* 3.2 34.1 + - + -
28B GLY* 4.8 2.3 - - - -
29B ASP* 4.4 14.1 + - - +
51B ASP* 5.1 2.0 - - - +
53B ASP* 3.1 11.3 + - + +
55B ASP* 1.3 75.5 - - - +
57B LEU* 1.3 59.5 + - - +
59B GLY* 3.2 1.4 + - - -
60B GLU* 2.6 63.9 + - + +
243D MET 3.7 20.0 + - - +
244D LYS* 4.2 11.4 - - + +
246D TYR* 5.1 6.5 + - - -
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Residues in contact with LEU 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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27B VAL* 3.1 43.7 - - + -
49B LEU* 3.4 23.1 - - + +
50B VAL 5.0 0.2 - - - -
51B ASP* 3.1 26.0 + - + +
53B ASP 3.5 5.7 + - - +
54B THR 4.1 2.0 - - - +
55B ASP 3.0 2.6 + - - -
56B LYS* 1.3 74.8 - - - +
58B ARG* 1.3 48.8 + - - +
59B GLY 2.6 9.8 + - - -
60B GLU* 2.8 2.9 + - + -
61B ALA* 2.6 35.7 + - + +
78B PHE* 3.1 56.8 - - + -
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Residues in contact with ARG 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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54B THR* 3.3 15.8 + - - +
55B ASP 3.2 5.2 + - - +
57B LEU* 1.3 71.0 - - - +
59B GLY* 1.3 57.4 + - - +
61B ALA* 4.2 2.2 - - - -
62B LEU* 3.0 32.2 - - + +
78B PHE* 2.9 41.1 - - + -
243D MET* 2.9 25.6 - - + +
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Residues in contact with GLY 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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55B ASP 3.4 4.0 + - - -
56B LYS 3.2 4.8 + - - -
57B LEU 2.6 6.7 + - - -
58B ARG* 1.3 75.2 - - - +
60B GLU* 1.3 57.5 + - - -
62B LEU* 3.2 5.6 + - - +
63B ASP* 3.0 27.0 + - - +
240D VAL* 4.1 8.4 - - - +
243D MET* 3.4 29.4 - - - -
244D LYS* 4.4 10.3 - - - -
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Residues in contact with GLU 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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27B VAL* 4.4 2.5 - - + -
32B MET* 3.2 40.0 - - + +
56B LYS* 2.6 65.6 + - + +
57B LEU* 3.6 4.3 - - + +
59B GLY* 1.3 69.0 - - - -
61B ALA* 1.3 66.1 + - - +
63B ASP* 3.1 11.6 + - - +
64B LEU* 3.1 17.8 + - - +
244D LYS* 2.3 48.0 + - + +
246D TYR* 4.5 4.5 + - - -
249D TRP* 3.6 7.3 + - - -
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Residues in contact with ALA 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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32B MET* 4.8 0.4 - - - +
49B LEU* 3.4 33.2 - - + -
57B LEU* 2.6 25.7 + - + +
58B ARG* 4.2 2.0 - - - -
60B GLU* 1.3 72.6 - - - +
62B LEU* 1.3 50.9 + - + +
64B LEU* 2.9 13.8 + - - +
65B GLN* 2.8 38.5 + - - +
76B ILE* 4.6 4.6 - - + +
78B PHE* 3.9 13.9 - - + -
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Residues in contact with LEU 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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58B ARG* 3.0 36.7 + - + +
59B GLY* 3.2 6.9 + - - +
61B ALA* 1.3 74.4 - - + +
63B ASP* 1.3 60.7 - - - +
65B GLN* 3.5 24.6 - - + +
66B HIS* 2.8 56.7 + - + +
171D TYR* 4.9 5.8 - - + +
239D GLU* 5.7 5.8 - - + -
240D VAL* 5.5 4.7 - - + -
243D MET* 4.2 11.7 - - + -
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Residues in contact with ASP 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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59B GLY 3.0 12.9 + - - +
60B GLU 3.1 11.7 - - - +
61B ALA 3.1 0.2 - - - -
62B LEU* 1.3 76.6 - - - +
64B LEU* 1.3 66.2 + - - +
65B GLN 3.2 0.2 + - - -
66B HIS* 3.3 7.6 + - - +
67B GLY* 3.1 17.2 + - - -
168D ARG* 5.5 1.0 + - - -
240D VAL* 4.1 18.4 - - + +
244D LYS* 2.8 15.5 + - - +
247D THR* 5.3 1.7 + - - -
248D SER* 2.7 36.5 + - - -
249D TRP* 3.5 11.5 + - + -
250D ALA* 3.5 23.1 + - - +
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Residues in contact with LEU 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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32B MET* 4.2 13.2 - - + -
35B ALA* 4.7 6.7 - - + -
36B ILE* 4.3 9.9 - - + +
39B LEU* 3.7 31.9 - - + -
47B LEU* 5.1 1.3 - - + -
49B LEU* 4.1 25.6 - - + -
60B GLU 3.1 10.0 + - - +
61B ALA* 2.9 8.8 + - - +
63B ASP* 1.3 77.3 - - - +
65B GLN* 1.3 53.9 + - - +
67B GLY* 2.8 27.8 + - - -
68B SER* 3.2 4.3 + - - -
71B LEU* 4.2 11.5 - - + +
76B ILE* 4.6 16.4 - - + -
249D TRP* 2.8 40.8 - - + +
253D LEU* 5.6 2.5 - - + -
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Residues in contact with GLN 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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61B ALA* 2.8 16.6 + - - +
62B LEU* 3.8 22.9 - - + +
63B ASP 3.1 0.2 - - - -
64B LEU* 1.3 71.3 - - - +
66B HIS* 1.3 54.3 + - - +
67B GLY 2.8 3.6 - - - -
68B SER* 2.7 39.7 + - - +
76B ILE* 2.5 45.5 - - + +
77B VAL* 4.7 1.2 - - - +
171D TYR* 3.2 36.8 + - + +
175D GLU* 5.3 0.2 + - - -
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Residues in contact with HIS 66 (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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62B LEU* 2.8 40.5 + - + +
63B ASP* 3.3 8.6 + - - +
65B GLN* 1.3 72.8 - - - +
67B GLY* 1.3 59.2 - - - +
68B SER* 3.3 0.7 + - - -
69B LEU* 4.9 1.4 + - - +
167D ALA* 4.3 11.3 - - - +
168D ARG* 2.8 50.2 + - + +
171D TYR* 4.0 37.0 - + - +
172D LEU* 5.1 7.5 - - + +
236D GLY* 3.1 36.7 - - - -
240D VAL* 3.9 10.1 - - + +
250D ALA* 4.6 6.7 - - + +
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Residues in contact with GLY 67 (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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63B ASP 3.1 8.2 + - - -
64B LEU* 2.8 14.6 + - - -
65B GLN 2.7 1.2 + - - -
66B HIS* 1.3 77.4 - - - +
68B SER* 1.3 67.4 + - - +
69B LEU* 3.0 10.6 + - - +
70B PHE* 3.7 6.9 + - - +
71B LEU* 3.9 10.2 - - - +
250D ALA* 4.4 14.1 - - - -
253D LEU* 5.1 9.3 - - - +
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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