Contacts of the helix formed by residues 53 - 68 (chain B) in PDB entry 3K4H
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 THR 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLU* 1.3 80.9 - - + +
54B GLU* 1.3 63.8 + - - +
55B GLU* 2.9 30.2 + - - +
56B GLU* 2.7 38.4 + - - +
57B ILE* 3.1 24.4 + - - +
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Residues in contact with GLU 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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53B THR* 1.3 74.3 - - - +
55B GLU* 1.3 67.1 + - + +
57B ILE* 3.7 10.3 + - - +
58B PHE* 3.2 20.4 + - - +
79B ARG* 4.5 29.2 + - - +
83B ARG* 2.7 40.8 + - - +
84B ILE* 5.7 2.2 - - + +
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Residues in contact with GLU 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 THR* 2.9 29.7 + - - +
54B GLU* 1.3 82.4 + - + +
56B GLU* 1.3 64.6 + - - +
58B PHE* 3.1 7.9 + - - +
59B ASN* 2.8 38.8 + - - +
83B ARG* 4.8 7.6 - - - +
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Residues in contact with GLU 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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51B GLY* 4.0 14.7 + - - -
52B GLU* 2.6 35.1 + - - +
53B THR* 2.7 35.1 + - - +
55B GLU* 1.3 83.3 - - - +
57B ILE* 1.3 63.7 + - - +
59B ASN* 3.2 13.1 + - - +
60B GLY* 3.0 19.9 + - - -
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Residues in contact with ILE 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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14B VAL* 3.9 20.6 - - + -
15B MSE 4.3 8.3 - - - +
17B SER* 4.4 9.0 - - - +
49B SER* 5.0 8.5 - - - +
51B GLY* 3.9 28.0 - - - +
52B GLU 4.3 7.4 - - - +
53B THR 3.1 19.3 + - - +
54B GLU* 3.9 8.1 - - - +
56B GLU* 1.3 74.5 - - - +
58B PHE* 1.3 65.9 + - - +
60B GLY* 3.0 11.9 + - - -
61B VAL* 3.1 13.3 + - + +
77B TYR* 3.2 28.5 - - - +
84B ILE* 4.0 13.0 - - + -
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Residues in contact with PHE 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 GLU* 3.2 12.9 + - - +
55B GLU* 3.1 9.3 + - - +
57B ILE* 1.3 78.8 - - - +
59B ASN* 1.3 71.9 + - - +
61B VAL* 3.3 6.3 + - + +
62B VAL* 3.1 38.5 + - + +
83B ARG* 3.6 65.1 - - + +
84B ILE* 3.7 27.1 - - + +
87B TYR* 3.8 39.5 - + + -
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Residues in contact with ASN 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 GLU* 2.8 22.3 + - - +
56B GLU* 3.4 16.2 - - - +
57B ILE 3.2 0.2 - - - -
58B PHE* 1.3 81.6 - - - +
60B GLY* 1.3 52.7 + - - +
62B VAL* 2.9 12.6 + - - +
63B LYS* 2.8 34.2 + - - +
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Residues in contact with GLY 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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47B TYR* 5.1 1.0 + - - -
49B SER* 5.6 9.4 - - - -
56B GLU 3.0 13.2 + - - -
57B ILE* 3.0 5.7 + - - -
59B ASN* 1.3 76.0 - - - +
61B VAL* 1.3 61.2 + - - +
63B LYS* 3.0 11.3 + - - +
64B MSE 2.9 29.2 + - - +
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Residues in contact with VAL 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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14B VAL* 3.6 31.2 - - + -
57B ILE 3.1 13.4 + - - +
58B PHE* 3.5 8.7 - - + +
60B GLY* 1.3 73.5 - - - +
62B VAL* 1.3 64.9 + - - +
64B MSE 2.9 21.9 + - - +
65B VAL* 3.0 19.6 + - + +
73B ILE* 3.9 9.4 - - + -
84B ILE* 3.9 24.9 - - + -
87B TYR* 4.3 7.2 - - + -
88B LEU* 3.5 31.4 - - + -
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Residues in contact with VAL 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 PHE* 3.1 39.5 + - + +
59B ASN* 2.9 12.6 + - - +
61B VAL* 1.3 77.4 - - - +
63B LYS* 1.3 56.9 + - - +
65B VAL* 3.9 1.0 - - - +
66B GLN* 3.0 62.1 + - - +
87B TYR* 3.9 27.1 - - + +
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Residues in contact with LYS 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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47B TYR* 4.9 11.9 - - - +
59B ASN 2.8 14.7 + - - +
60B GLY* 3.0 13.0 + - - +
62B VAL* 1.3 74.2 - - - +
64B MSE 1.3 55.9 + - - +
66B GLN* 4.1 4.0 - - - +
67B GLY* 2.9 27.8 + - - -
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Residues in contact with MSE 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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12B GLY* 3.0 38.6 - - - -
13B LEU 5.0 3.8 - - - +
14B VAL* 4.7 13.0 - - - -
47B TYR* 3.6 30.7 - - + -
49B SER* 5.4 6.1 - - - -
60B GLY 2.9 18.5 + - - +
61B VAL* 2.9 16.6 + - - +
63B LYS* 1.3 78.4 - - - +
65B VAL* 1.3 62.9 + - - +
67B GLY* 3.5 1.0 + - - -
68B ARG* 3.4 14.2 + - - -
69B GLN* 4.6 0.5 + - - +
70B ILE* 3.1 42.4 + - + +
73B ILE* 3.5 30.3 - - + -
93B PHE* 5.5 0.9 - - + -
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Residues in contact with VAL 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 VAL* 3.0 23.8 - - + +
62B VAL 3.9 2.2 - - - +
64B MSE 1.3 71.7 - - - +
66B GLN* 1.3 68.5 + - + +
68B ARG* 3.1 19.6 + - - +
73B ILE* 4.5 11.0 - - + -
87B TYR* 3.9 24.7 - - + +
88B LEU* 4.7 3.8 - - + -
91B GLN* 4.2 26.5 - - + +
93B PHE* 3.6 37.6 - - + -
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Residues in contact with GLN 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 VAL* 3.0 32.4 + - - +
63B LYS* 4.1 4.2 - - - +
65B VAL* 1.3 81.9 - - - +
67B GLY* 1.3 63.0 + - - +
68B ARG* 3.3 12.2 + - - +
87B TYR* 3.2 21.9 + - - +
91B GLN* 5.3 4.3 + - - +
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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 LYS 2.9 18.4 + - - -
64B MSE 4.0 1.3 - - - -
65B VAL 3.2 0.4 - - - -
66B GLN* 1.3 74.3 - - - +
68B ARG* 1.3 67.4 + - - +
69B GLN* 3.1 21.0 + - - +
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Residues in contact with ARG 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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8B THR* 5.1 4.0 + - - +
64B MSE 3.4 6.1 + - - -
65B VAL 3.1 18.4 + - - +
66B GLN 3.9 9.4 - - - +
67B GLY* 1.3 78.6 - - - +
69B GLN* 1.3 64.5 + - - +
70B ILE 3.5 6.6 - - - +
93B PHE* 6.2 1.3 - - - -
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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