Contacts of the helix formed by residues 46 - 60 (chain B) in PDB entry 3D5K
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B PHE* 4.5 0.9 - - - +
45B ARG* 1.3 76.0 - - - +
47B PRO* 1.3 69.9 - - - +
48B GLN* 2.7 37.2 + - - +
49B LEU* 3.9 11.0 - - + +
50B GLN* 3.2 24.5 + - - +
165B TYR* 2.7 30.6 + - + -
249B GLY* 3.5 2.3 - - - -
250B LEU* 3.0 39.6 + - + +
256B LEU* 5.0 4.0 - - + +
477B NA 3.2 17.8 - - - -
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Residues in contact with PRO 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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41B ARG* 5.4 0.3 + - - -
45B ARG 3.3 8.9 - - - +
46B ASP* 1.3 87.5 - - - +
48B GLN* 1.3 63.3 + - - +
50B GLN* 3.5 15.9 + - + +
51B GLN* 3.1 22.7 + - - +
247B PRO* 4.2 22.0 - - + +
248B GLN 3.5 19.7 - - - +
250B LEU* 4.6 9.4 - - + -
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Residues in contact with GLN 48 (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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46B ASP* 2.7 18.0 + - - +
47B PRO* 1.3 72.7 - - - +
49B LEU* 1.3 60.4 + - - +
51B GLN* 3.2 5.4 + - - +
52B LEU* 2.9 37.9 + - + +
165B TYR* 3.8 24.4 - - - +
242B ILE* 5.7 1.4 - - - +
246B LEU* 3.9 28.9 - - + +
247B PRO* 3.1 33.8 - - - +
248B GLN* 4.7 0.2 - - - -
249B GLY* 3.5 14.1 + - - -
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Residues in contact with LEU 49 (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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44B PHE* 3.7 29.4 - - + -
46B ASP* 3.4 13.9 + - + +
48B GLN* 1.3 73.9 - - - +
50B GLN* 1.3 56.8 + - - +
52B LEU* 3.2 8.6 + - + -
53B ILE* 2.8 56.2 + - + +
161B VAL* 4.0 8.7 - - + -
162B ALA* 3.9 23.3 - - + +
165B TYR* 3.9 47.2 - - + -
166B LEU* 5.4 5.4 - - + -
257B LEU* 5.8 0.2 - - + -
477B NA 4.0 11.4 - - - -
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Residues in contact with GLN 50 (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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40B TRP* 3.3 21.7 - - + -
41B ARG* 2.8 60.9 + - - +
44B PHE* 2.5 38.4 + - + +
45B ARG* 3.9 10.1 + - - +
46B ASP 3.2 13.9 + - - +
47B PRO* 3.5 15.8 - - - +
49B LEU* 1.3 78.7 - - - +
51B GLN* 1.3 62.3 + - - +
53B ILE* 4.6 1.6 - - - -
54B GLY* 3.1 17.5 + - - -
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Residues in contact with GLN 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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41B ARG* 4.6 4.9 - - - +
47B PRO 3.1 9.7 + - - +
48B GLN 3.5 8.1 - - - +
50B GLN* 1.3 78.2 - - - +
52B LEU* 1.3 58.6 + - - +
54B GLY* 3.1 4.7 + - - -
55B VAL* 3.0 37.8 + - + +
243B PRO* 4.6 8.9 - - - +
245B ASN* 4.1 18.1 + - - +
246B LEU* 3.7 21.4 - - + +
247B PRO* 3.4 24.2 - - + +
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Residues in contact with LEU 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 GLN* 2.9 28.6 + - + +
49B LEU* 3.2 8.5 + - + +
51B GLN* 1.3 76.3 - - - +
53B ILE* 1.3 56.2 + - - +
55B VAL* 3.3 5.1 + - - +
56B ALA* 3.1 21.7 + - - +
161B VAL* 4.4 8.1 - - + -
165B TYR* 3.6 36.6 - - + -
234B LEU* 4.6 11.9 - - + -
238B LEU* 3.3 37.6 - - + +
242B ILE* 4.5 5.2 - - + -
243B PRO* 3.8 29.2 - - + -
246B LEU* 4.1 11.9 - - + -
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Residues in contact with ILE 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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40B TRP* 3.7 32.5 - - + -
44B PHE* 3.6 38.1 - - + -
49B LEU* 2.8 36.7 + - + +
50B GLN* 3.7 4.5 - - - +
52B LEU* 1.3 69.8 - - - +
54B GLY* 1.3 61.5 + - - +
56B ALA* 3.1 5.8 + - + +
57B LEU* 3.0 35.9 + - + +
158B VAL* 4.2 22.7 - - + +
161B VAL* 3.9 25.1 - - + -
162B ALA* 5.2 0.2 - - + -
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Residues in contact with GLY 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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40B TRP* 3.9 10.9 - - - -
41B ARG* 5.8 1.8 - - - -
50B GLN 3.1 13.4 + - - -
51B GLN* 3.1 6.0 + - - -
53B ILE* 1.3 78.1 - - - +
55B VAL* 1.3 59.2 + - - +
57B LEU* 3.6 8.0 + - - +
58B GLU* 3.6 19.4 + - - +
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Residues in contact with VAL 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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51B GLN* 3.0 25.5 + - + +
52B LEU* 3.5 9.4 - - - +
53B ILE 3.2 0.4 - - - -
54B GLY* 1.3 75.7 - - - +
56B ALA* 1.3 61.1 - - - +
58B GLU* 3.4 2.2 + - - -
59B ASN* 3.0 39.6 + - - +
238B LEU* 4.4 15.3 - - + +
240B SER* 3.7 23.6 - - - +
241B GLY 4.9 1.8 - - - +
243B PRO* 3.9 29.8 - - + -
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Residues in contact with ALA 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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52B LEU 3.1 11.4 + - - +
53B ILE* 3.1 8.0 + - + +
55B VAL* 1.3 74.8 - - - +
57B LEU* 1.3 61.8 + - + +
60B ASN* 2.9 33.5 + - - +
63B LEU* 4.8 0.2 - - - +
157B LEU* 3.8 10.3 - - + +
161B VAL* 3.7 30.7 - - + -
237B LEU 3.8 12.1 - - - +
238B LEU* 3.4 14.8 - - - +
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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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40B TRP* 3.6 33.9 - - + -
53B ILE* 3.0 20.9 + - + +
54B GLY* 3.9 7.4 - - - +
55B VAL 3.4 0.4 - - - -
56B ALA* 1.3 76.4 - - + +
58B GLU* 1.3 58.1 + - - +
60B ASN 5.0 1.2 + - - +
63B LEU* 3.9 25.4 - - + +
154B GLN* 3.7 33.2 - - + +
157B LEU* 4.5 6.7 - - + -
158B VAL* 4.2 13.5 - - + -
452B GLN* 5.9 0.4 - - - +
479B NA 3.7 17.5 - - - -
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Residues in contact with GLU 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 GLY 3.6 11.0 + - - +
55B VAL* 3.4 2.2 + - - -
56B ALA 3.2 0.4 - - - -
57B LEU* 1.3 78.2 - - - +
59B ASN* 1.3 69.1 + - - +
60B ASN 5.4 0.4 - - - -
64B ARG* 2.7 33.3 + - - +
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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 VAL* 3.0 32.5 + - - +
58B GLU* 1.3 98.3 + - - +
60B ASN* 1.3 65.7 + - - +
61B ARG* 2.6 32.4 + - - +
64B ARG* 3.9 10.3 + - - +
238B LEU 3.2 18.6 - - - +
239B GLY* 3.8 14.7 - - - +
240B SER* 4.1 11.0 + - - +
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Residues in contact with ASN 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 ALA 2.9 23.0 + - - +
57B LEU 5.4 0.9 - - - +
58B GLU 4.0 0.9 - - - -
59B ASN* 1.3 71.5 - - - +
61B ARG* 1.3 58.6 + - - +
62B ASP* 2.9 37.3 + - - +
63B LEU* 3.2 12.0 + - + +
64B ARG* 3.2 24.4 + - - +
157B LEU* 3.4 29.4 - - + +
236B LEU 4.1 4.2 + - - -
237B LEU* 2.7 39.6 + - - +
238B LEU 3.5 4.5 + - - -
239B GLY* 4.3 4.3 - - - -
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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