Contacts of the helix formed by residues 46 - 55 (chain B) in PDB entry 4DKE
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 GLN 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ARG 3.4 12.0 + - - +
43B ASP* 3.1 30.6 + - - +
44B LYS 3.2 0.2 - - - -
45B LEU* 1.3 77.4 - - - +
47B TYR* 1.3 69.1 + - - +
48B ARG* 3.2 36.2 + - - +
49B SER* 2.7 39.5 + - - +
50B ARG* 3.3 2.1 + - - +
169B PHE* 4.6 4.3 - - - -
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Residues in contact with TYR 47 (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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45B LEU 3.5 2.4 + - - -
46B GLN* 1.3 70.6 - - - +
48B ARG* 1.3 66.3 + - + +
49B SER 3.0 0.3 + - - -
50B ARG* 3.2 35.9 + - - +
51B LEU* 2.8 62.8 + - + +
162B LYS* 4.3 20.5 + - - -
169B PHE* 5.3 1.2 - - - -
170B ARG* 6.3 0.7 - - - -
64H LYS* 4.3 20.4 + - - +
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 2.9 37.3 + - - +
47B TYR* 1.3 85.7 - - + +
49B SER* 1.3 59.4 - - - +
51B LEU* 3.5 11.5 - - + +
52B GLN* 3.0 27.0 + - - +
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP 4.8 0.3 + - - -
44B LYS 3.4 21.9 + - - -
46B GLN* 2.7 38.3 + - - +
48B ARG* 1.3 71.5 - - - +
50B ARG* 1.3 56.3 + - - -
51B LEU 3.1 1.1 - - - -
52B GLN* 2.9 9.3 + - - +
53B TYR* 2.8 45.8 + - - +
118B TYR* 3.9 11.3 - - - -
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 2.7 53.2 + - + +
46B GLN 4.0 0.7 - - - +
47B TYR* 3.5 42.2 - - - +
49B SER* 1.3 76.0 - - - +
51B LEU* 1.3 63.5 + - - +
54B MET* 2.9 38.9 + - + +
55B LYS 3.7 0.7 + - - -
118B TYR* 4.1 6.9 + - - +
162B LYS* 4.2 10.2 - - + +
165B LEU* 4.1 14.1 - - + -
166B ASP* 2.8 47.2 + - - +
169B PHE* 3.3 36.5 - - - -
170B ARG* 5.1 9.1 - - - +
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Residues in contact with LEU 51 (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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47B TYR* 2.8 52.9 + - + +
48B ARG* 3.5 12.1 - - + +
50B ARG* 1.3 79.5 - - - +
52B GLN* 1.3 57.9 + - - +
55B LYS* 3.3 27.9 - - + +
56B HIS* 2.9 63.1 + - + +
162B LYS* 4.4 14.5 - - - +
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Residues in contact with GLN 52 (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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48B ARG 3.0 16.7 + - - +
49B SER* 2.9 9.7 + - - +
51B LEU* 1.3 77.7 - - - +
53B TYR* 1.3 86.2 + - - +
56B HIS* 3.5 13.6 + - + +
57B TYR* 2.8 71.9 + - + -
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Residues in contact with TYR 53 (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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49B SER* 2.8 30.4 + - - +
52B GLN* 1.3 98.2 + - - +
54B MET* 1.3 71.9 + - + +
55B LYS 3.4 0.4 + - - -
57B TYR* 3.4 31.1 + + - +
58B PHE* 3.3 12.8 - - - -
114B PRO* 3.8 15.3 - - + -
115B SER* 2.6 27.6 + - - +
118B TYR* 3.0 55.6 - + + -
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Residues in contact with MET 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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50B ARG* 2.9 20.6 + - - +
53B TYR* 1.3 116.7 - - + +
55B LYS* 1.3 59.7 + - - +
58B PHE* 3.7 17.4 - - + +
105B VAL* 4.4 8.7 - - - -
115B SER* 3.8 14.8 - - - -
118B TYR* 4.4 2.9 - - + -
119B LEU* 4.1 17.7 - - + -
161B PRO* 3.6 27.1 - - - +
162B LYS* 3.4 32.2 + - - +
165B LEU* 3.2 41.1 - - + -
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Residues in contact with LYS 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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110A LEU* 3.7 19.4 - - + +
51B LEU* 3.3 32.8 + - + +
53B TYR 3.4 1.6 + - - -
54B MET* 1.3 81.2 - - - +
56B HIS* 1.3 73.2 + - + +
57B TYR 3.1 1.6 - - - -
58B PHE* 3.0 24.6 + - - +
59B PRO 4.6 1.2 - - - +
160B ARG* 6.4 3.1 - - - +
162B LYS* 4.3 19.9 - - + +
56H TYR* 3.0 39.4 + - - -
57H SER 5.1 1.4 + - - -
58H ASP* 4.1 5.9 + - - -
64H LYS* 5.6 5.5 - - - +
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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