Contacts of the helix formed by residues 54 - 62 (chain B) in PDB entry 2HPD
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 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLU* 3.0 40.3 + - - +
52B LEU* 4.9 0.4 - - - +
53B SER* 1.3 84.2 - - - +
55B GLN* 1.3 64.5 + - - +
56B ARG* 3.9 5.3 + - - -
57B LEU* 3.6 15.3 + - - +
58B ILE* 3.0 25.2 + - - +
360B LEU* 3.9 3.4 - - - -
363B ASP* 3.4 12.8 - - - -
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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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243A PRO* 5.8 3.0 - - - +
54B SER* 1.3 69.5 - - - +
56B ARG* 1.3 69.0 + - - +
58B ILE* 3.1 2.4 + - - +
59B LYS* 3.0 54.3 + - - +
360B LEU* 3.7 15.9 - - + +
363B ASP* 2.9 17.0 + - + +
366B ILE* 3.8 32.5 - - + +
386B PRO* 4.3 11.7 - - - +
387B GLN* 2.9 22.8 + - - +
388B HIS* 4.1 6.1 - - + +
389B ALA* 4.0 20.6 - - + -
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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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38B GLU* 2.8 39.3 + - - +
54B SER* 4.0 8.5 - - - +
55B GLN* 1.3 81.3 + - - +
57B LEU* 1.3 75.8 + - - +
59B LYS* 3.6 33.1 - - - +
60B GLU* 3.9 9.7 + - - +
342B GLY* 3.5 28.0 + - - -
344B GLU* 3.0 32.1 + - - -
345B TYR* 4.8 0.4 - - - -
363B ASP* 4.6 0.6 + - - -
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Residues in contact with LEU 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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38B GLU* 3.8 20.0 - - - +
39B ILE* 3.7 42.4 - - + -
52B LEU* 4.1 14.7 - - + +
54B SER* 3.6 13.2 + - - +
55B GLN 3.2 0.2 - - - -
56B ARG* 1.3 104.0 - - - +
58B ILE* 1.3 57.7 + - - +
59B LYS 3.3 0.7 - - - -
60B GLU* 3.3 8.3 + - - +
61B ALA* 3.0 26.2 + - - +
341B LEU* 4.0 23.5 - - + +
342B GLY* 4.1 17.0 - - - +
345B TYR* 4.8 6.1 - - + -
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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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52B LEU* 3.6 36.1 - - + +
53B SER 3.8 4.3 - - - -
54B SER 3.0 28.7 + - - +
55B GLN* 3.1 1.5 + - - +
57B LEU* 1.3 73.5 - - - +
59B LYS* 1.3 64.9 + - - +
61B ALA* 3.1 5.7 + - - +
62B CYS* 3.0 44.3 + - - -
355B VAL* 3.5 32.3 - - + -
360B LEU* 3.8 24.9 - - + -
388B HIS* 4.7 3.1 - - + +
391B LYS* 4.2 15.3 - - + -
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Residues in contact with LYS 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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243A PRO* 4.2 25.4 - - + +
55B GLN* 3.0 43.7 + - - +
56B ARG* 3.6 24.4 + - - +
58B ILE* 1.3 76.0 - - - +
60B GLU* 1.3 66.8 + - - +
62B CYS* 3.5 9.9 + - - +
63B ASP* 4.0 4.9 + - - +
387B GLN* 4.2 7.9 - - + +
388B HIS* 3.8 36.6 + - + +
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Residues in contact with GLU 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 3.9 8.6 + - - +
57B LEU* 3.3 12.1 + - - +
58B ILE 3.2 0.4 - - - -
59B LYS* 1.3 84.4 - - - +
61B ALA* 1.3 62.2 + - - +
62B CYS 3.1 1.2 + - - -
63B ASP* 3.2 21.8 + - - +
66B ARG* 3.1 36.3 + - - +
67B PHE* 3.9 7.7 - - - -
340B VAL 3.6 1.6 - - - +
341B LEU* 3.7 9.1 - - + +
342B GLY* 2.9 41.1 + - - -
343B GLY 4.2 0.3 + - - -
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Residues in contact with ALA 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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52B LEU* 3.7 23.8 - - + -
57B LEU 3.0 15.8 + - - +
58B ILE* 3.1 6.0 + - - +
60B GLU* 1.3 75.1 - - - +
62B CYS* 1.3 55.4 + - - +
63B ASP 3.2 4.2 + - - -
67B PHE* 3.4 27.0 - - + +
333B LEU* 3.4 31.4 - - + +
341B LEU* 4.2 2.9 - - + +
353B LEU* 4.2 12.1 - - + -
355B VAL* 5.5 0.7 - - + -
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Residues in contact with CYS 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* 3.0 26.8 + - - +
59B LYS 3.8 8.1 - - - +
60B GLU 3.1 1.2 + - - -
61B ALA* 1.3 76.0 - - - +
63B ASP* 1.3 60.4 + - - +
64B GLU* 3.3 5.4 + - - +
67B PHE 5.7 0.4 - - - -
331B PHE* 4.6 7.2 - - - -
333B LEU* 5.2 3.4 - - - -
388B HIS* 3.9 16.4 + - + +
391B LYS* 3.7 25.1 - - - -
395B ASN* 3.0 49.4 + - - +
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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