Contacts of the helix formed by residues 56 - 70 (chain B) in PDB entry 5LDH
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 GLU 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 7.4 - - - +
55B LEU* 1.3 86.5 - - - +
57B ASP* 1.3 80.6 + - - +
59B LEU* 3.1 17.7 - - - +
60B LYS* 3.1 11.8 + - - +
83B LYS* 4.2 23.1 + - - +
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Residues in contact with ASP 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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241A LYS* 4.6 10.5 - - + -
242A LEU* 2.9 23.0 - - + +
55B LEU* 4.5 7.2 - - - +
56B GLU* 1.3 91.3 + - - +
58B LYS* 1.3 86.1 + - - +
59B LEU 2.8 1.8 - - - -
60B LYS* 2.6 20.9 + - - +
61B GLY 3.1 3.1 + - - -
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Residues in contact with LYS 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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242A LEU* 2.9 25.2 - - + +
245A TYR* 3.0 31.4 - - + +
29B VAL* 5.4 2.0 - - + -
30B GLY* 5.2 3.8 - - - -
31B GLN* 5.5 8.3 - - - +
55B LEU* 4.9 9.6 - - + -
57B ASP* 1.3 87.1 - - - +
59B LEU* 1.3 57.9 + - + +
61B GLY 3.0 0.5 + - - -
62B GLU* 2.4 44.9 + - + +
332B LNC 3.5 30.1 + - - +
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Residues in contact with LEU 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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29B VAL* 4.3 23.1 - - + -
51B LEU* 5.4 3.8 - - + +
52B VAL* 4.7 2.9 - - - -
53B ASP* 4.1 19.3 - - + +
55B LEU* 2.3 68.9 - - + +
56B GLU* 3.1 9.4 - - - +
57B ASP 2.8 0.4 + - - -
58B LYS* 1.3 81.3 - - - +
60B LYS* 1.3 70.8 + - + +
62B GLU* 4.6 0.2 - - - +
63B MET* 2.9 23.5 + - - +
80B ALA* 5.3 6.5 - - + -
81B ASN* 3.6 33.7 - - - +
83B LYS* 4.6 1.1 - - + -
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Residues in contact with LYS 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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241A LYS* 6.2 3.8 - - + -
242A LEU* 5.3 0.7 - - + -
56B GLU 3.1 9.0 + - - +
57B ASP* 2.6 15.2 + - - +
59B LEU* 1.3 78.6 - - + +
61B GLY* 1.3 62.4 + - - +
63B MET* 3.5 12.2 + - + +
64B MET* 3.0 42.0 + - + +
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Residues in contact with GLY 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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239A VAL* 3.7 20.6 - - - +
242A LEU* 3.5 19.8 - - - +
245A TYR* 3.2 17.2 - - - +
57B ASP 3.1 3.8 + - - -
58B LYS 3.0 5.8 + - - -
60B LYS* 1.3 80.4 - - - +
62B GLU* 1.3 62.7 + - - +
64B MET* 3.2 18.5 + - - +
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Residues in contact with GLU 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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245A TYR* 1.5 81.7 - - + +
248A TRP* 2.9 2.1 + - - -
29B VAL* 3.7 24.9 - - + +
30B GLY* 5.4 1.1 - - - -
34B MET* 2.4 47.1 - - + +
51B LEU* 6.3 0.4 - - + -
58B LYS* 2.4 37.0 + - + +
59B LEU 3.6 2.5 - - - +
61B GLY* 1.3 67.9 - - - +
63B MET* 1.3 58.2 + - - +
65B ASP* 3.4 6.2 + - - +
66B LEU* 2.7 29.5 + - - +
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Residues in contact with MET 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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51B LEU* 4.7 10.9 - - + +
59B LEU 2.9 17.7 + - - +
60B LYS* 4.0 12.6 - - + +
62B GLU* 1.3 72.2 - - - +
64B MET* 1.3 60.8 + - - +
66B LEU* 2.7 14.6 + - - -
67B GLN* 2.3 63.6 + - + +
78B ILE* 3.0 37.9 - - + +
80B ALA* 3.2 36.8 - - + +
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Residues in contact with MET 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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235A SER* 5.4 5.4 - - - +
238A GLU* 5.9 1.3 - - - +
239A VAL* 3.9 33.9 - - + -
245A TYR 5.6 0.7 - - - +
60B LYS* 3.0 52.3 + - + +
61B GLY* 3.2 15.1 + - - +
63B MET* 1.3 86.2 - - - +
65B ASP* 1.3 53.8 + - - +
67B GLN* 4.4 7.4 - - - +
68B HIS* 2.4 71.2 + - + +
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Residues in contact with ASP 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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245A TYR* 1.5 42.2 + - + +
246A THR* 2.6 2.4 - - - +
248A TRP* 1.9 43.9 + - + -
249A ALA* 0.9 91.3 + - - +
252A LEU* 5.0 0.5 - - - +
61B GLY 3.6 0.8 + - - -
62B GLU 3.4 1.8 + - - +
63B MET 3.1 0.4 - - - -
64B MET* 1.3 76.6 - - - +
66B LEU* 1.3 62.8 + - - +
68B HIS* 4.1 1.3 - - - -
69B GLY* 2.9 20.4 + - - -
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Residues in contact with LEU 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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248A TRP* 4.6 9.2 - - + -
252A LEU* 5.3 7.5 - - + +
34B MET* 2.4 43.7 - - + -
37B ALA* 4.8 9.6 - - + -
38B ILE* 4.3 23.8 - - + -
41B LEU* 4.8 17.7 - - + -
51B LEU* 4.8 12.1 - - + -
62B GLU 2.7 23.0 + - - +
63B MET* 2.7 11.7 + - + +
65B ASP* 1.3 79.4 - - - +
67B GLN* 1.3 65.3 + - - +
69B GLY* 3.0 13.5 + - - -
70B SER* 3.1 8.0 + - - -
78B ILE* 5.7 4.7 - - + -
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Residues in contact with GLN 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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174A TYR* 2.3 55.2 + - + -
178A GLU* 5.5 0.2 + - - -
63B MET* 2.3 65.9 + - + +
64B MET* 4.0 9.0 - - - +
66B LEU* 1.3 67.9 - - - +
68B HIS* 1.3 56.4 + - + +
70B SER* 2.2 44.6 + - - +
78B ILE* 4.0 23.3 + - + +
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Residues in contact with HIS 68 (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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167A LEU* 5.3 4.0 - - + -
170A ALA* 4.2 20.6 - - + +
171A ARG* 3.5 45.9 + - - +
174A TYR* 5.0 15.9 - + - +
235A SER* 4.7 14.3 + - - -
239A VAL* 6.0 0.2 - - + -
246A THR* 6.4 0.6 - - - -
249A ALA* 3.9 9.9 - - + +
64B MET* 2.4 67.6 + - + +
65B ASP* 3.7 6.1 + - - +
67B GLN* 1.3 76.4 + - + +
69B GLY* 1.3 72.2 + - - +
70B SER* 2.7 9.3 + - - -
71B LEU* 3.7 2.4 + - - +
72B PHE* 5.4 0.9 - - - -
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Residues in contact with GLY 69 (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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249A ALA* 4.1 3.3 - - - +
252A LEU* 3.6 29.4 - - - -
65B ASP 2.9 13.3 + - - -
66B LEU 3.0 5.3 + - - -
68B HIS* 1.3 76.3 - - - +
70B SER* 1.3 52.4 + - - +
71B LEU* 2.4 21.8 + - - +
72B PHE* 2.6 30.5 + - - +
73B LEU* 4.9 1.3 - - - -
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Residues in contact with SER 70 (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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174A TYR* 4.7 18.8 - - - -
184A PRO* 6.0 4.9 - - - +
66B LEU 3.1 6.8 + - - -
67B GLN* 2.2 30.4 + - - +
68B HIS 2.7 4.9 - - - -
69B GLY* 1.3 73.4 - - - +
71B LEU* 1.3 58.5 + - - -
72B PHE 3.0 1.6 + - - -
73B LEU* 2.4 33.7 + - - +
75B THR* 5.1 9.9 + - - +
76B PRO 5.3 4.3 + - - -
78B ILE* 5.8 2.8 - - - +
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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