Contacts of the helix formed by residues 52 - 62 (chain B) in PDB entry 4H3E
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 SER 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY* 3.5 4.9 - - - -
51B PHE* 1.3 75.4 - - - +
53B PRO* 1.3 75.0 - - - +
54B ARG* 3.5 7.5 + - - +
55B GLN 3.0 16.8 + - - -
56B MET* 3.1 17.0 + - - +
202B LYS* 4.2 1.9 - - - +
203B ASP* 2.7 33.6 + - - -
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Residues in contact with PRO 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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43B TRP* 3.6 9.2 - - + +
44B LYS* 3.4 27.4 - - - +
45B ASP* 4.0 4.3 - - - +
46B GLY* 3.5 17.9 - - - +
51B PHE 4.5 0.4 - - - +
52B SER* 1.3 88.8 - - - +
54B ARG* 1.3 56.9 + - - +
56B MET 3.3 0.3 + - - -
57B GLU* 2.8 31.2 + - - +
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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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205A GLU* 2.9 41.5 + - - +
206A ASN* 5.6 0.4 + - - -
52B SER* 3.2 7.2 + - - +
53B PRO* 1.3 77.0 - - - +
55B GLN* 1.3 66.0 + - - +
57B GLU* 2.8 44.3 + - - +
58B LEU* 2.9 45.8 + - + +
62B LYS* 5.3 7.5 - - - +
202B LYS* 3.9 19.1 - - + +
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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
----------------------------------------------------------
201A TYR* 5.0 1.6 + - - -
51B PHE* 3.8 13.7 - - + -
52B SER* 3.0 12.7 + - - +
54B ARG* 1.3 75.2 - - - +
56B MET* 1.3 66.0 + - + +
58B LEU* 3.9 6.0 - - - +
59B HIS* 3.1 21.0 + - - +
198B HIS 3.1 23.6 + - - -
199B ALA* 3.3 17.6 + - - +
200B TYR* 3.1 15.8 - - - -
202B LYS* 3.0 37.9 + - + +
203B ASP* 3.1 34.6 + - - +
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Residues in contact with MET 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 6.0 0.9 - - + -
41B PHE* 4.3 9.4 - - + -
43B TRP* 3.9 21.1 - - + +
46B GLY 3.7 22.0 - - - +
47B CYS* 3.8 16.4 - - - +
51B PHE* 3.5 35.2 - - + -
52B SER 3.1 13.8 + - - +
53B PRO 3.7 5.8 - - - +
55B GLN* 1.3 80.1 - - + +
57B GLU* 1.3 66.4 + - - +
59B HIS* 3.9 13.8 - - + +
60B TYR* 2.9 30.1 + - + +
113B TYR* 5.4 1.8 - - - +
114B PHE* 4.7 9.8 - - + -
117B ILE* 4.1 15.7 - - + -
199B ALA 5.2 0.7 - - - +
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Residues in contact with GLU 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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43B TRP* 3.5 40.1 - - + -
53B PRO 2.8 21.3 + - - +
54B ARG* 2.8 41.2 + - - +
56B MET* 1.3 71.9 - - - +
58B LEU* 1.3 57.8 + - - +
61B THR* 2.6 49.5 + - - +
62B LYS* 5.4 4.8 - - - -
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Residues in contact with LEU 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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201A TYR* 3.6 36.6 - - + +
205A GLU* 3.7 23.3 - - + +
206A ASN* 3.6 24.0 - - - +
54B ARG* 2.9 49.7 + - - +
55B GLN* 3.9 5.2 - - - +
57B GLU* 1.3 78.0 - - - +
59B HIS* 1.3 63.6 + - - +
62B LYS* 3.1 20.7 + - + +
63B HIS* 3.0 23.0 + - + -
202B LYS* 4.1 16.6 - - + -
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Residues in contact with HIS 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 GLN* 3.1 21.1 + - - +
56B MET* 3.9 8.8 - - + +
58B LEU* 1.3 79.2 - - - +
60B TYR* 1.3 58.5 + - - +
63B HIS* 3.4 8.2 - - + +
64B HIS* 2.9 26.7 + - - +
110B HIS* 3.3 12.7 + + - -
113B TYR* 3.5 26.4 + + - -
114B PHE* 3.7 11.7 - + + -
194B ASP* 2.8 15.7 + - - -
198B HIS* 3.3 15.6 + + - +
199B ALA* 3.4 30.3 + - + -
301B FE2 2.3 27.2 - - - -
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Residues in contact with TYR 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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36B LEU* 3.6 32.4 + - + +
37B PRO 2.6 34.1 + - - -
38B LYS* 3.5 10.4 - - - +
39B LEU* 3.8 33.6 + - + -
43B TRP* 3.6 34.8 - + + -
56B MET* 2.9 17.8 + - + +
57B GLU* 5.1 0.2 - - - -
59B HIS* 1.3 76.7 - - - +
61B THR* 1.3 69.6 + - + +
62B LYS 3.3 0.4 + - - -
64B HIS* 3.3 11.8 - - - +
65B LYS* 3.1 26.9 + - - +
114B PHE* 4.0 20.0 - + + -
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Residues in contact with THR 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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36B LEU* 4.8 3.4 - - + -
43B TRP* 3.9 30.5 - - + +
57B GLU* 2.6 37.0 + - - +
60B TYR* 1.3 93.2 - - + +
62B LYS* 1.3 76.5 + - - +
65B LYS* 3.3 29.7 - - - +
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Residues in contact with LYS 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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206A ASN* 3.8 39.9 - - + +
54B ARG* 5.3 9.0 - - - +
57B GLU* 5.4 4.3 - - - -
58B LEU* 3.1 31.1 + - + +
61B THR* 1.3 95.5 + - - +
63B HIS* 1.3 62.9 + - - +
65B LYS* 3.9 0.5 - - - +
66B ALA* 2.9 32.2 + - - +
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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