Contacts of the helix formed by residues 41 - 54 (chain B) in PDB entry 3HJW
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 TYR 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASP* 3.2 1.6 + - - -
40B PRO* 1.3 103.4 - - + +
42B GLY* 1.3 55.5 + - - +
43B GLU 3.1 2.9 - - - -
44B TYR* 2.9 19.5 + + + +
45B ARG* 2.7 38.6 + - + +
38C ASN* 4.9 6.7 - - - -
41C THR* 3.4 15.7 - - + -
42C LYS* 2.4 37.8 + - - -
45C GLU* 3.0 34.3 + - - -
66C HIS* 3.8 39.0 - + + -
70C LEU* 5.4 1.6 - - + -
21D G 4.1 3.9 + - - -
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 3.3 33.0 + - - -
40B PRO 3.5 0.6 - - - -
41B TYR* 1.3 75.9 - - - +
43B GLU* 1.3 51.3 + - - +
45B ARG* 3.7 14.2 - - - +
46B ARG* 2.6 54.8 + - - +
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Residues in contact with GLU 43 (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 PRO 5.1 2.6 + - - +
41B TYR* 3.1 1.1 - - - -
42B GLY* 1.3 75.8 - - - +
44B TYR* 1.3 84.3 + - + +
46B ARG* 3.3 22.9 + - - +
47B ARG* 2.9 52.4 + - - +
50B ARG* 4.5 3.4 + - - +
73C GLU* 4.9 1.6 - - - +
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Residues in contact with TYR 44 (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 PRO 5.3 2.0 - - - -
41B TYR* 2.9 21.7 + + + +
43B GLU* 1.3 100.5 + - + +
45B ARG* 1.3 65.4 + - - +
47B ARG* 3.2 26.6 + - - +
48B TRP* 3.2 16.8 + - - +
45C GLU* 5.5 2.7 - - - -
66C HIS* 3.8 22.4 - - + +
69C PRO* 3.6 15.4 - - + +
70C LEU* 3.6 41.7 - - + +
73C GLU* 2.8 46.9 + - + +
74C LYS* 4.8 4.7 + - - -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A HIS* 3.7 26.5 + - - +
224A VAL* 3.8 9.3 - - - +
225A ASP* 2.6 42.2 + - - +
35B PHE* 4.6 0.6 - - - -
39B ASP* 2.8 42.8 + - - -
41B TYR* 2.7 21.1 + - + +
42B GLY* 3.7 15.8 - - - +
44B TYR* 1.3 71.9 - - - +
46B ARG* 1.3 56.2 + - - +
48B TRP* 3.2 28.6 + - + -
49B LYS* 2.9 29.5 + - - +
62C GLU* 4.0 25.1 - - + +
65C ALA* 5.4 2.0 - - + -
66C HIS* 4.1 13.9 - - + +
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Residues in contact with ARG 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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224A VAL* 5.0 0.2 - - - +
225A ASP* 3.3 27.2 + - - +
228A TYR* 3.4 51.8 - - - -
229A PHE* 3.5 18.6 - - + -
232A GLU* 5.2 5.3 + - - -
39B ASP* 3.9 9.3 + - - -
42B GLY* 2.6 42.2 + - - +
43B GLU* 3.3 33.4 - - - +
45B ARG* 1.3 75.5 - - - +
47B ARG* 1.3 55.1 + - - +
49B LYS* 3.8 5.2 - - - +
50B ARG* 2.9 58.2 + - - +
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Residues in contact with ARG 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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43B GLU* 2.9 48.1 + - - +
44B TYR* 3.5 33.6 + - - +
45B ARG 3.2 0.6 - - - -
46B ARG* 1.3 73.2 - - - +
48B TRP* 1.3 64.8 + - - +
50B ARG* 3.7 16.1 + - + +
51B GLU* 3.3 22.3 + - - +
69C PRO* 4.3 19.2 + - + -
73C GLU* 4.1 21.0 + - - +
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Residues in contact with TRP 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 TYR 3.2 6.9 + - - +
45B ARG* 3.2 35.6 + - + +
47B ARG* 1.3 78.3 - - - +
49B LYS* 1.3 78.9 + - + +
51B GLU* 3.2 9.4 + - - +
52B VAL* 3.0 39.6 + - + +
6C SER* 3.2 30.2 + - - -
7C TYR* 3.8 14.3 - - - +
9C LYS* 3.9 22.4 - - - +
61C GLU* 3.7 20.2 - - + -
62C GLU* 4.3 20.9 - - + -
65C ALA* 3.7 43.3 - - + +
69C PRO* 4.1 10.4 - - + +
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Residues in contact with LYS 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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221A HIS* 3.9 9.3 + - - +
222A ASP* 2.7 36.9 + - - +
225A ASP* 2.8 37.7 + - + +
226A TYR* 4.4 6.3 - - + +
229A PHE* 4.2 10.3 - - + -
45B ARG* 2.9 17.0 + - - +
46B ARG* 3.8 7.4 - - - +
48B TRP* 1.3 98.8 - - + +
50B ARG* 1.3 60.8 + - - +
52B VAL* 3.3 9.8 + - + +
53B LEU* 3.0 49.8 + - + +
62C GLU* 4.4 6.0 + - - -
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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
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228A TYR* 5.4 2.2 + - - +
229A PHE* 3.6 20.2 - - + -
232A GLU* 5.4 4.0 + - - -
233A ASP* 2.8 37.6 + - - -
43B GLU* 4.5 3.8 + - - +
46B ARG* 2.9 63.1 + - - +
47B ARG* 3.8 17.8 - - + +
48B TRP 3.3 0.2 - - - -
49B LYS* 1.3 74.3 - - - +
51B GLU* 1.3 62.3 + - - +
53B LEU 3.4 2.1 + - - -
54B GLY 3.5 0.5 + - - -
55B ILE* 3.2 54.9 + - + +
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Residues in contact with GLU 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 ARG 3.3 10.6 + - - +
48B TRP* 3.2 12.0 + - - +
50B ARG* 1.3 79.8 - - - +
52B VAL* 1.3 62.7 - - + +
53B LEU 3.5 0.3 + - - -
54B GLY* 3.8 7.4 + - - -
9C LYS* 3.3 38.6 + - - +
72C GLU* 5.8 0.2 - - - +
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Residues in contact with VAL 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 TRP* 3.0 43.6 + - + +
49B LYS* 3.3 12.8 + - + +
51B GLU* 1.3 80.4 - - + +
53B LEU* 1.3 68.3 + - + +
54B GLY 3.3 1.7 + - - -
6C SER* 3.9 22.2 - - - +
9C LYS* 5.8 0.9 - - - +
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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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226A TYR* 4.0 21.5 - - + +
229A PHE* 3.8 26.9 - - + -
238A TYR* 3.5 41.7 + - + +
49B LYS* 3.0 30.3 + - + +
50B ARG 3.4 0.4 + - - -
51B GLU 3.3 0.4 - - - -
52B VAL* 1.3 86.4 - - + +
54B GLY* 1.3 61.4 + - - +
55B ILE* 3.3 11.3 + - + -
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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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50B ARG 3.5 3.5 + - - -
51B GLU 3.8 5.8 + - - -
52B VAL 3.3 4.9 + - - -
53B LEU* 1.3 78.4 - - - +
55B ILE* 1.3 63.9 + - - +
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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