Contacts of the helix formed by residues 48 - 54 (chain B) in PDB entry 5H1C
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 THR 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PRO* 5.0 1.3 - - + -
23B GLN 3.0 22.7 - - - +
24B PRO* 4.6 0.9 - - + -
25B ILE* 3.7 6.2 - - - +
47B HIS* 1.3 88.8 + - + +
49B VAL* 1.3 65.9 + - - +
50B GLU* 4.1 4.7 + - - +
51B ALA* 3.0 31.0 + - - +
52B VAL* 3.3 13.7 + - - +
208B SER 5.9 0.4 - - - +
212B VAL* 4.4 16.4 - - + -
258B GLU* 3.9 2.3 + - - -
259B PHE* 3.4 36.6 - - + -
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Residues in contact with VAL 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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23B GLN* 2.4 45.6 + - + +
24B PRO 3.4 17.0 - - - +
27B ARG* 4.3 2.7 - - + -
28B LEU* 3.6 38.4 - - + -
48B THR 1.3 67.1 - - - -
50B GLU* 1.3 58.2 + - - +
52B VAL* 3.1 5.9 + - - +
53B ALA* 2.9 23.7 + - - +
78B ALA* 4.5 10.9 - - - +
81B LEU* 3.6 39.0 - - + -
82B VAL* 4.7 3.4 - - + -
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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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22B PRO* 3.8 30.9 - - - +
23B GLN* 4.2 16.9 + - + +
48B THR* 3.2 4.8 - - - +
49B VAL* 1.3 77.1 - - - +
51B ALA* 1.3 58.9 + - - +
53B ALA* 2.9 9.7 + - - +
54B TYR* 2.9 55.9 + - + +
82B VAL* 3.6 23.3 - - + +
258B GLU* 4.2 25.0 - - + +
259B PHE* 4.7 0.5 - - - -
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Residues in contact with ALA 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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46B PHE* 4.6 23.9 - - + -
47B HIS 4.8 0.7 - - - +
48B THR* 3.0 26.5 + - - +
50B GLU* 1.3 78.6 - - - +
52B VAL* 1.3 62.3 + - - +
54B TYR* 3.3 4.2 + - - +
55B ALA* 3.1 22.6 + - - +
254B ARG* 5.0 11.0 + - - -
258B GLU* 3.1 23.4 + - - +
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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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25B ILE* 4.9 8.3 - - + -
28B LEU* 4.2 17.7 - - + -
41B LEU* 5.8 7.0 - - + -
46B PHE* 4.4 23.1 - - + -
48B THR 3.7 11.9 - - - +
49B VAL 3.1 8.0 + - - +
51B ALA* 1.3 77.1 - - - +
53B ALA* 1.3 63.5 + - - +
55B ALA* 3.2 22.3 + - - +
60B LEU* 4.5 10.1 - - + -
74B ILE* 3.5 31.9 - - + -
75B LEU* 4.0 9.8 - - + +
78B ALA* 4.3 11.4 - - + -
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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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195A PHE* 5.5 0.7 - - - +
196A ASN* 3.8 11.4 + - - -
49B VAL 2.9 12.3 + - - +
50B GLU* 2.9 16.1 + - - +
52B VAL* 1.3 80.3 - - - +
54B TYR* 1.3 71.9 + - + +
55B ALA 3.3 1.2 + - - -
75B LEU* 5.5 2.5 - - - +
78B ALA* 3.7 29.2 - - + +
82B VAL* 4.4 10.1 - - + -
84B MET* 5.2 9.5 - - + +
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Residues in contact with TYR 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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195A PHE* 3.3 61.1 - + + +
196A ASN* 2.7 22.2 - - - +
50B GLU* 2.9 44.4 + - + +
51B ALA* 3.3 5.6 + - - +
52B VAL 3.2 0.2 - - - -
53B ALA* 1.3 86.3 - - + +
55B ALA* 1.3 54.5 + - - +
56B PRO* 3.5 5.0 - - - +
82B VAL* 4.1 13.5 - - + +
84B MET* 3.9 17.0 - - + -
250B ARG* 4.6 4.9 + - - -
254B ARG* 5.2 14.2 + - + -
257B ASP* 4.6 12.2 + - + -
258B GLU* 4.0 23.6 - - + +
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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