Contacts of the helix formed by residues 45 - 59 (chain B) in PDB entry 1D7K
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 LEU 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.8 8.3 - - + -
11B CYS* 4.0 28.9 - - + -
43B ALA* 3.3 1.3 + - + +
44B ASP* 1.3 68.7 - - - +
46B GLY* 1.3 64.7 + - - +
48B ILE* 3.1 21.0 + - + +
49B LEU* 3.1 20.3 + - - +
75B ALA* 4.2 3.8 - - + +
76B ILE* 3.7 30.5 - - + -
79B THR* 3.7 28.0 - - + +
407B TYR* 3.8 28.3 - - + -
408B VAL 3.0 12.1 + - - +
409B MET* 4.0 16.2 - - + -
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Residues in contact with GLY 46 (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 ASP* 3.0 13.4 + - - -
45B LEU* 1.3 78.1 - - - +
47B ASP* 1.3 58.5 + - - +
49B LEU* 3.6 2.9 + - - +
50B LYS* 3.1 32.2 + - - +
409B MET* 3.9 9.7 - - - +
410B SER* 5.1 0.9 - - - -
413B ALA* 3.5 27.6 - - - -
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Residues in contact with ASP 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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44B ASP* 2.9 30.0 + - + +
46B GLY* 1.3 75.6 - - - +
48B ILE* 1.3 59.4 + - - +
50B LYS* 3.5 9.6 + - - +
51B LYS* 3.0 35.5 + - - +
279B TYR 5.0 0.7 - - - +
282B SER* 2.6 32.0 + - - -
283B ALA* 3.1 23.0 + - - +
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Residues in contact with ILE 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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44B ASP 3.7 5.4 - - - +
45B LEU* 3.4 15.5 - - + +
47B ASP* 1.3 81.7 - - - +
49B LEU* 1.3 61.0 + - - +
51B LYS* 3.2 12.6 + - - +
52B HIS* 3.3 10.7 + - - +
76B ILE* 3.5 34.3 - - + -
79B THR* 5.0 9.0 - - + -
80B LEU* 4.0 29.2 - - + +
279B TYR* 3.7 25.8 - - + +
280B VAL* 4.1 15.5 - - + -
283B ALA* 3.6 26.9 - - + -
284B PHE* 5.1 0.2 - - + -
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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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45B LEU 3.1 25.3 + - - +
46B GLY* 3.9 8.5 - - - +
48B ILE* 1.3 71.8 - - - +
50B LYS* 1.3 65.5 + - - +
52B HIS* 3.5 6.5 + - + +
53B LEU* 3.4 19.8 + - - +
79B THR* 3.5 27.8 - - + -
80B LEU* 6.3 2.0 - - + -
83B THR* 3.5 24.9 - - - +
409B MET* 3.6 22.2 - - + -
413B ALA* 4.5 5.2 - - + +
416B LEU* 4.3 16.9 - - + +
417B MET* 3.8 33.2 - - + +
420B PHE* 4.4 9.1 - - + -
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Residues in contact with LYS 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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46B GLY 3.1 22.6 + - - +
47B ASP* 3.7 13.9 - - - +
48B ILE 3.3 0.2 - - - -
49B LEU* 1.3 73.6 - - - +
51B LYS* 1.4 68.4 + - + +
53B LEU* 3.4 9.6 + - + +
54B ARG* 3.1 23.3 + - - +
410B SER* 5.7 1.3 - - - -
412B PRO* 5.8 3.0 - - - +
413B ALA* 4.7 13.2 - - - +
416B LEU* 3.6 23.8 - - + -
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Residues in contact with LYS 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 ASP* 3.0 25.4 + - - +
48B ILE 3.2 7.4 + - - +
50B LYS* 1.4 77.2 - - + +
52B HIS* 1.3 57.3 + - - +
54B ARG* 3.4 21.4 + - - +
55B TRP 3.0 11.8 + - - -
239B PRO 5.8 0.2 - - - -
240B GLY 2.8 29.8 + - - -
241B SER* 5.5 1.8 - - - +
278B TYR* 2.5 77.4 + - + +
279B TYR* 3.8 21.0 + - + +
282B SER* 3.3 23.6 + - - +
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Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE 3.3 7.8 + - - +
49B LEU* 3.9 8.3 - - - +
50B LYS 3.2 0.8 - - - -
51B LYS* 1.3 75.5 - - - +
53B LEU* 1.3 65.4 - - - +
55B TRP* 3.1 4.8 + + - +
56B LEU* 3.0 50.3 + - + +
64B PRO* 3.7 19.5 - - + -
80B LEU* 5.3 0.9 - - + -
83B THR* 3.3 44.9 + - + +
84B GLY 5.0 1.3 - - - -
85B THR* 3.8 13.8 + - + +
279B TYR* 2.6 39.5 + - + -
420B PHE* 4.3 11.2 - + + -
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Residues in contact with LEU 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 LEU 3.4 9.3 + - - +
50B LYS* 3.4 11.4 + - + +
51B LYS 3.3 0.4 - - - -
52B HIS* 1.3 78.4 - - - +
54B ARG* 1.3 63.7 + - - +
56B LEU* 3.2 28.8 + - + +
57B LYS* 3.3 30.9 + - - +
416B LEU* 3.4 40.8 - - + -
420B PHE* 5.4 11.8 - - + -
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Residues in contact with ARG 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 LYS 3.1 14.8 + - - +
51B LYS* 4.3 24.1 - - - +
52B HIS 3.2 0.2 - - - -
53B LEU* 1.3 82.9 - - - +
55B TRP* 1.3 55.3 + - - +
57B LYS* 3.8 11.4 + - - +
58B ALA* 3.2 25.8 + - - +
241B SER 6.1 1.2 - - - -
242B GLU* 2.9 34.5 + - - +
248B PHE* 4.1 16.4 - - + +
249B GLU* 2.8 42.5 + - - +
278B TYR* 3.2 19.4 - - - +
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Residues in contact with TRP 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 LYS 3.0 13.7 + - - +
52B HIS* 3.1 8.5 + - - +
54B ARG* 1.3 73.9 - - - +
56B LEU* 1.3 74.4 + - + +
59B LEU* 3.0 48.3 + - + +
62B VAL* 3.1 27.5 + - + -
64B PRO* 3.7 33.2 - - + +
238B PHE* 3.9 25.6 - + - -
248B PHE* 3.4 34.5 - + - -
273B ALA* 4.1 18.6 - - + -
275B PRO* 3.9 23.3 - - + -
278B TYR* 3.4 22.8 + + + +
279B TYR* 4.2 8.3 - - - +
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Residues in contact with LEU 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 HIS* 3.0 45.4 + - + +
53B LEU* 3.2 19.7 + - + +
55B TRP* 1.3 83.0 - - + +
57B LYS* 1.3 61.2 + - - +
59B LEU 4.7 2.2 - - - +
60B PRO* 3.5 25.3 - - + +
64B PRO* 5.8 3.1 - - + -
420B PHE* 4.5 15.9 - - + -
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Residues in contact with LYS 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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53B LEU* 3.3 29.5 + - + +
54B ARG* 4.2 10.0 - - - +
56B LEU* 1.3 78.8 - - - +
58B ALA* 1.3 62.6 + - - +
59B LEU 3.4 0.3 + - - -
60B PRO* 3.6 9.4 - - - +
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Residues in contact with ALA 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 ARG 3.2 18.1 + - - +
55B TRP 4.3 0.4 - - - +
56B LEU 3.4 0.4 - - - -
57B LYS* 1.3 79.0 - - - +
59B LEU* 1.3 63.5 + - - +
60B PRO* 3.5 2.5 - - - -
248B PHE* 3.7 27.1 - - + -
249B GLU* 4.5 10.1 - - + +
252B THR* 3.9 18.0 + - + +
256B ASN* 3.1 21.0 + - - -
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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
----------------------------------------------------------
55B TRP* 3.0 62.6 + - + +
56B LEU* 4.0 1.4 - - - +
58B ALA* 1.3 89.5 - - + +
60B PRO* 1.3 66.4 - - - +
61B ARG 3.2 4.0 - - - -
62B VAL* 3.2 35.0 + - + +
234B ILE* 5.2 1.3 - - + -
238B PHE* 4.5 8.7 - - + -
248B PHE* 4.2 6.5 - - + -
252B THR* 3.7 25.6 - - + -
255B ILE* 4.1 19.3 - - + -
256B ASN* 4.0 15.9 - - - +
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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