Contacts of the helix formed by residues 42 - 55 (chain B) in PDB entry 2H3W
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 PRO 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B VAL 4.3 1.3 - - - +
41B PRO* 1.3 85.7 - - + +
43B LEU* 1.3 65.7 + - - +
44B GLN* 4.5 2.7 - - + +
45B GLN* 3.4 39.2 - - + +
46B SER 3.2 17.3 + - - -
84B GLN* 4.0 2.7 - - - +
88B GLU* 5.9 0.4 - - - +
519B HIS* 3.7 2.9 - - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO 3.5 1.8 + - - -
42B PRO* 1.3 72.6 - - - +
44B GLN* 1.3 64.2 + - - +
46B SER* 3.4 1.7 + - - -
47B LEU* 3.0 43.8 + - + +
73B PHE* 4.1 7.6 - - + -
74B GLN* 3.7 24.5 - - + +
80B GLY* 3.7 30.3 - - - +
81B GLU* 3.9 8.1 - - + +
84B GLN* 3.6 28.1 + - + +
519B HIS* 4.1 3.1 - - + -
523B LEU* 3.8 28.7 - - + -
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.4 3.6 - - + +
43B LEU* 1.3 78.8 - - - +
45B GLN* 1.3 57.4 + - - +
47B LEU* 3.8 0.9 - - - +
48B ASP* 2.9 32.7 + - + +
74B GLN* 3.3 33.8 + - - +
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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
----------------------------------------------------------
41B PRO* 3.8 21.8 - - - +
42B PRO* 3.3 36.4 + - + +
43B LEU 3.2 0.2 - - - -
44B GLN* 1.3 79.9 - - - +
46B SER* 1.3 61.9 + - - +
48B ASP* 3.2 6.4 + - - +
49B TYR* 3.1 45.9 + - + -
514B GLU* 3.8 39.2 + - - +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.3 15.9 - - - +
42B PRO 3.2 2.8 + - - -
43B LEU* 4.0 1.1 - - - -
45B GLN* 1.3 76.3 + - - +
47B LEU* 1.3 62.1 + - - +
49B TYR* 3.4 5.4 + - - +
50B TYR* 2.9 28.1 + - - +
514B GLU 5.2 0.2 + - - -
515B ALA 3.9 2.9 + - - -
516B PHE* 3.5 29.5 - - - +
519B HIS* 2.7 37.3 + - - -
520B LEU* 5.0 7.1 - - - +
523B LEU* 6.2 0.2 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.0 33.8 + - + +
44B GLN 3.8 4.0 - - - +
46B SER* 1.3 75.3 - - - +
48B ASP* 1.3 62.1 + - - +
50B TYR* 3.3 9.5 + - + +
51B LEU* 3.1 29.8 + - - +
70B VAL* 3.9 20.4 - - + -
73B PHE* 3.9 15.3 - - + -
74B GLN* 3.4 40.8 - - + +
520B LEU* 4.1 20.9 - - + -
537B ILE* 3.9 26.9 - - + -
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Residues in contact with ASP 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 GLN* 2.9 22.4 + - + +
45B GLN* 3.4 7.6 - - - +
47B LEU* 1.3 76.3 - - - +
49B TYR* 1.3 71.9 + - - +
51B LEU* 3.3 12.6 + - - +
52B LYS* 2.7 54.5 + - - +
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Residues in contact with TYR 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* 3.1 41.8 + - + +
46B SER* 3.8 5.2 - - - +
48B ASP* 1.3 84.7 - - - +
50B TYR* 1.3 66.4 - - - +
52B LYS* 3.2 15.8 + - + +
53B ALA* 2.9 24.8 + - - +
506B TYR* 5.7 3.7 - + + +
509B ARG* 3.2 48.9 + - - -
514B GLU* 3.9 24.8 + - + -
515B ALA* 5.5 0.4 - - - -
516B PHE* 3.6 21.7 - + + -
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Residues in contact with TYR 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 SER 2.9 14.4 + - - +
47B LEU* 3.3 14.8 - - + +
49B TYR* 1.3 76.4 - - - +
51B LEU* 1.3 63.4 + - - +
53B ALA* 3.1 3.8 + - - +
54B LEU* 3.0 61.5 + - + +
66B THR* 4.0 11.9 - - + +
70B VAL* 4.5 12.6 - - + -
469B ARG* 5.7 0.2 - - - -
516B PHE* 3.5 32.9 - + + -
520B LEU* 3.8 17.5 - - + -
537B ILE* 4.5 21.5 + - + -
540B ASP* 4.7 0.7 + - - -
542B SER* 3.7 2.4 - - - -
543B TYR* 3.3 47.1 + + - +
546B ALA* 4.3 7.9 - - + -
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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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47B LEU 3.1 13.7 + - - +
48B ASP* 3.3 11.4 + - - +
50B TYR* 1.3 79.6 - - + +
52B LYS* 1.3 63.6 + - + +
54B LEU* 3.3 11.0 + - + -
55B GLN* 3.3 3.7 + - - +
63B TRP* 2.8 44.1 + - + +
66B THR* 3.9 15.5 - - + -
67B LYS* 3.6 50.5 - - + +
70B VAL* 3.8 37.7 - - + -
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Residues in contact with LYS 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 ASP* 2.7 46.9 + - - +
49B TYR* 3.2 20.3 + - + +
50B TYR 3.2 1.0 - - - -
51B LEU* 1.3 77.9 - - + +
53B ALA* 1.3 61.9 + - - +
54B LEU 3.4 0.3 + - - -
55B GLN* 3.5 27.8 + - - +
56B PRO* 3.5 9.9 - - - +
472B SER* 5.2 0.4 - - - -
473B ILE* 3.7 18.9 + - + +
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Residues in contact with ALA 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 TYR 2.9 16.9 + - - +
50B TYR* 3.1 4.2 + - + +
52B LYS* 1.3 75.8 - - - +
54B LEU* 1.3 61.5 + - + +
56B PRO* 3.5 14.9 - - - +
57B ILE* 3.9 12.4 - - - +
469B ARG* 3.8 34.7 - - + -
471B ALA 3.9 10.1 - - - +
472B SER* 5.4 3.4 - - - +
506B TYR* 4.8 6.5 - - + +
516B PHE* 3.9 9.2 - - + -
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Residues in contact with LEU 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 TYR* 3.0 49.5 + - + +
51B LEU* 3.7 11.2 - - + +
52B LYS 3.2 0.6 - - - -
53B ALA* 1.3 78.3 - - - +
55B GLN* 1.3 65.4 + - - +
56B PRO 3.3 0.9 - - - -
57B ILE* 2.9 20.4 + - + +
58B VAL* 3.1 30.9 + - + +
63B TRP* 4.0 8.1 - - + -
66B THR* 3.6 26.7 - - + -
542B SER* 3.6 27.6 - - - +
546B ALA* 3.7 18.8 - - + -
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Residues in contact with GLN 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 LEU 3.4 3.1 - - - +
52B LYS* 3.6 17.2 - - - +
54B LEU* 1.3 77.2 - - - +
56B PRO* 1.3 68.7 - - + +
57B ILE 3.4 0.5 + - - -
58B VAL* 3.5 14.8 - - - +
63B TRP* 3.2 42.7 - - + +
473B ILE* 3.4 32.3 - - + +
476B LEU* 5.2 1.0 - - - +
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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