Contacts of the helix formed by residues 43 - 64 (chain B) in PDB entry 1HNW
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 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TYR 3.1 12.5 + - - +
33B TYR* 3.6 33.4 - - + +
41B ILE 3.5 2.2 + - - -
42B ILE* 1.3 70.5 - - - +
44B LEU* 1.3 57.4 + - - +
45B GLN* 2.7 43.4 + - - +
46B LYS* 3.2 41.5 + - + +
47B THR* 3.1 21.9 + - - -
202B PRO* 5.4 0.3 - - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.3 8.1 - - + +
12B GLU* 4.2 13.7 - - + +
13B ALA* 4.0 29.6 - - + +
16B HIS* 4.5 5.8 - - + -
17B PHE* 3.4 48.5 - - + +
42B ILE 3.4 1.9 + - - +
43B ASP* 1.3 68.9 + - - +
45B GLN* 1.3 68.0 + - + +
46B LYS 2.9 2.2 - - - -
47B THR* 3.1 28.4 - - + +
48B MET* 2.8 31.1 + - + +
202B PRO 4.8 1.1 - - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.3 6.7 - - + -
33B TYR* 5.0 15.8 + - - -
43B ASP* 2.7 28.3 + - - +
44B LEU* 1.3 72.9 - - + +
46B LYS* 1.3 57.8 + - + +
48B MET* 3.2 23.4 - - - +
49B GLU* 3.4 18.0 - - - +
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Residues in contact with LYS 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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30B ARG* 2.8 29.6 + - - +
31B TYR* 4.4 20.6 - - + -
32B ILE 4.3 8.9 + - - -
33B TYR* 5.8 0.2 - - - +
43B ASP* 3.2 36.7 + - + +
44B LEU 2.9 0.2 - - - -
45B GLN* 1.3 76.9 - - + +
47B THR* 1.3 54.4 + - - +
48B MET 2.7 15.5 + - - -
49B GLU* 2.8 29.8 + - + +
50B GLU* 3.0 14.9 + - + +
202B PRO* 4.7 2.0 - - + -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 5.8 3.4 - - + -
42B ILE* 3.6 4.3 - - - +
43B ASP 3.1 13.1 + - - -
44B LEU* 2.9 35.9 + - + +
46B LYS* 1.3 75.7 - - - +
48B MET* 1.3 58.6 + - - +
50B GLU* 4.0 2.6 - - - +
51B LEU* 3.1 35.2 + - + +
201B ILE* 4.7 6.7 - - + -
202B PRO* 2.9 46.0 + - + +
203B GLY* 5.0 1.8 - - - -
214B ILE* 5.8 3.8 - - + -
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 5.6 4.3 - - + -
9B GLU 3.2 27.6 - - - +
10B LEU* 3.2 46.7 - - + +
12B GLU* 6.1 2.0 - - - -
44B LEU* 2.8 22.4 + - + +
45B GLN* 3.2 11.2 - - - +
46B LYS 2.7 0.6 + - - -
47B THR* 1.3 76.0 - - - +
49B GLU* 1.3 55.5 + - + +
50B GLU 2.7 6.0 + - - -
51B LEU* 2.7 39.4 + - - +
52B GLU* 2.9 14.1 + - - +
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Residues in contact with GLU 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 GLN* 3.4 18.6 - - - +
46B LYS* 2.8 25.0 + - + +
48B MET* 1.3 77.0 - - + +
50B GLU* 1.3 64.7 + - + +
52B GLU* 3.8 15.7 - - - +
53B ARG* 3.5 20.6 + - - +
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Residues in contact with GLU 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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31B TYR* 4.1 30.7 + - + +
46B LYS 3.0 11.9 + - - +
47B THR 4.1 0.4 - - - +
48B MET 2.7 5.3 + - - -
49B GLU* 1.3 78.7 - - + +
51B LEU* 1.3 52.2 + - - +
52B GLU 3.2 0.2 - - - -
53B ARG* 3.3 28.9 + - - +
54B THR* 2.6 42.4 + - - -
200B ILE* 3.0 30.9 + - - +
202B PRO* 3.8 20.2 - - + -
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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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8B LYS 5.7 4.3 - - - +
9B GLU 5.3 2.7 - - - +
47B THR* 3.1 30.0 + - + +
48B MET* 2.7 31.6 + - - +
50B GLU* 1.3 69.9 - - - +
52B GLU* 1.3 60.7 + - - +
54B THR* 2.9 5.2 + - - -
55B PHE* 2.5 70.5 + - + +
200B ILE 4.6 0.4 + - - -
201B ILE* 3.7 25.6 - - + -
214B ILE* 4.4 14.8 - - + -
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Residues in contact with GLU 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 MET 2.9 13.2 + - - +
49B GLU* 3.8 15.1 - - - +
51B LEU* 1.3 80.1 - - - +
53B ARG* 1.3 58.6 + - - +
55B PHE* 4.1 2.4 - - - +
56B ARG* 2.9 45.3 + - + +
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Residues in contact with ARG 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 GLU 3.5 14.9 + - - +
50B GLU* 3.3 25.0 + - - +
51B LEU 3.3 0.2 - - - -
52B GLU* 1.3 80.7 - - - +
54B THR* 1.3 62.0 + - - +
56B ARG* 3.4 30.0 + - - +
57B PHE* 3.3 19.9 + - - +
198B ASP 3.6 17.4 + - - -
199B TYR* 2.7 52.1 - - + +
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Residues in contact with THR 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 GLU* 2.6 30.9 + - - -
51B LEU* 2.9 5.5 + - - -
53B ARG* 1.3 70.3 + - - +
55B PHE* 1.3 67.0 + - - +
56B ARG 3.0 1.6 - - - -
57B PHE* 2.9 16.1 + - - +
58B ILE* 3.0 23.4 + - + +
185B ILE* 3.4 33.9 - - + -
199B TYR* 3.6 19.9 - - + +
200B ILE 3.1 17.0 + - - -
201B ILE* 4.0 16.2 - - + -
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Residues in contact with PHE 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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7B VAL* 5.8 6.1 - - + -
51B LEU* 2.5 56.0 + - + +
52B GLU* 4.2 2.2 - - - +
54B THR* 1.3 74.4 - - - +
56B ARG* 1.3 60.9 + - - +
58B ILE* 2.9 25.9 + - + +
59B GLU* 2.9 18.2 + - - +
201B ILE* 3.8 17.7 - - + -
214B ILE* 3.8 9.0 - - - -
217B ARG* 3.8 14.8 - - + -
218B ALA* 3.4 43.7 - - + -
221B LEU* 3.7 26.2 - - + +
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Residues in contact with ARG 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 GLU* 2.9 33.1 + - + +
53B ARG* 3.4 39.7 - - - +
55B PHE* 1.3 78.4 - - - +
57B PHE* 1.3 63.8 + - - +
59B GLU* 3.3 25.4 + - - +
60B ASP* 3.4 9.7 + - - +
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Residues in contact with PHE 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 ARG 3.3 5.6 + - - +
54B THR 2.9 10.8 + - - +
56B ARG* 1.3 78.1 - - - +
58B ILE* 1.3 66.6 + - + +
60B ASP* 2.9 34.9 - - + +
61B LEU* 3.3 38.8 + - + +
68B ILE* 5.8 0.2 - - + -
183B PRO* 3.6 22.7 - - + -
185B ILE* 4.1 17.5 - - + -
199B TYR* 3.3 64.6 - + + -
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Residues in contact with ILE 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 THR* 3.1 27.6 - - + +
55B PHE* 2.9 32.1 + - + +
57B PHE* 1.3 83.3 - - + +
59B GLU* 1.3 66.0 + - - +
60B ASP 3.1 0.2 + - - -
61B LEU* 3.3 5.6 + - - +
62B ALA* 2.7 24.5 + - + +
68B ILE* 3.8 24.9 - - + -
163B PHE* 5.1 7.2 - - + -
185B ILE* 4.8 11.7 - - + -
218B ALA* 4.3 19.1 - - + +
221B LEU* 4.8 6.5 - - + -
222B ILE* 4.2 20.4 - - + -
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Residues in contact with GLU 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 PHE 2.9 13.3 + - - +
56B ARG* 3.3 18.1 + - - +
58B ILE* 1.3 73.8 - - - +
60B ASP* 1.3 70.3 + - - +
62B ALA* 2.8 8.5 + - - -
63B MET* 2.7 33.7 + - + +
221B LEU* 3.3 29.5 - - + +
224B GLN 5.5 1.0 - - - +
225B ALA* 4.7 12.2 - - + +
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Residues in contact with ASP 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 ARG 3.4 5.6 + - - +
57B PHE* 2.9 26.6 + - - +
59B GLU* 1.3 84.7 - - - +
61B LEU* 1.3 74.3 + - - +
62B ALA 2.8 6.6 + - - -
63B MET* 3.5 3.2 - - - +
64B ARG* 2.8 70.6 + - - +
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Residues in contact with LEU 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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57B PHE* 3.3 28.2 + - + +
58B ILE* 3.3 8.1 + - - +
60B ASP* 1.3 86.3 + - - +
62B ALA* 1.3 58.0 + - - +
64B ARG* 3.7 10.0 - - + +
65B GLY 3.6 1.0 + - - -
66B GLY* 2.9 40.4 + - - +
68B ILE* 4.6 13.5 - - + -
160B ASP* 3.5 34.5 - - + +
161B ALA* 3.3 34.3 - - + -
183B PRO* 5.3 0.2 - - + -
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Residues in contact with ALA 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 ILE* 2.7 20.0 + - + +
59B GLU* 2.9 14.8 - - - +
60B ASP 2.8 1.4 + - - -
61B LEU* 1.3 69.0 - - - +
63B MET* 1.3 54.7 + - - +
64B ARG 2.8 3.9 + - - -
65B GLY* 2.7 28.4 + - - -
66B GLY 4.0 3.2 + - - +
68B ILE* 6.1 0.9 - - + +
90B MET* 6.5 0.4 - - - -
222B ILE* 4.1 27.1 - - + +
225B ALA* 4.1 13.0 - - + -
226B ARG* 3.8 17.6 + - - +
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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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59B GLU* 2.7 28.4 + - + +
60B ASP* 3.5 5.8 - - - +
62B ALA* 1.3 73.5 - - - +
64B ARG* 1.3 76.9 + - - +
65B GLY 3.2 1.0 + - - -
225B ALA* 3.3 27.9 + - + +
226B ARG* 4.8 1.1 - - - -
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Residues in contact with ARG 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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60B ASP* 2.8 67.3 + - - +
61B LEU* 3.7 13.7 - - + +
62B ALA 2.8 0.4 + - - -
63B MET* 1.3 99.1 - - + +
65B GLY* 1.3 61.3 + - - +
66B GLY* 4.5 1.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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