Contacts of the helix formed by residues 48 - 56 (chain U) in PDB entry 6CP3
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 LEU 48 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46U THR 3.1 7.8 - - - +
47U ARG* 1.3 96.7 - - + +
49U ALA* 1.3 65.7 + - - +
50U ARG* 3.2 3.1 - - - +
51U TYR* 3.2 35.9 + - + +
52U LYS* 3.4 6.6 + - - +
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Residues in contact with ALA 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ALA* 3.3 30.0 - - + +
45U ASN 4.5 0.2 - - - -
46U THR* 3.9 22.5 - - - +
48U LEU* 1.3 74.4 - - - +
50U ARG* 1.3 59.0 + - - +
52U LYS* 3.3 18.9 + - - +
53U ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ALA 4.3 11.2 - - - +
45U ASN* 4.6 17.4 - - + +
47U ARG* 4.0 29.0 + - - +
48U LEU* 3.2 0.9 - - - -
49U ALA* 1.3 76.0 - - - +
51U TYR* 1.3 58.4 + - - +
53U ALA* 3.8 7.4 - - - +
54U LYS* 2.9 33.4 + - - +
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Residues in contact with TYR 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U LEU* 3.2 28.5 + - + +
50U ARG* 1.3 79.2 - - - +
52U LYS* 1.3 57.0 + - - +
54U LYS* 4.8 6.3 - - - +
55U TYR* 2.9 65.4 + + - +
56U PHE* 3.6 29.0 - + - -
65U PRO* 3.7 22.6 + - + +
68U HIS* 4.5 8.0 - + + +
69U PHE* 5.4 0.9 + - - +
46X LEU* 5.7 3.6 - - + -
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Residues in contact with LYS 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U LEU 3.4 5.8 + - - +
49U ALA* 3.3 18.2 + - - +
51U TYR* 1.3 75.9 - - + +
53U ALA* 1.3 63.2 + - - +
56U PHE* 2.6 57.3 + - + +
57U ASP* 3.4 11.4 - - - +
45X THR* 4.5 6.5 + - - +
46X LEU* 3.4 28.4 - - + +
48X ASN 4.3 15.3 + - - +
49X ASN* 5.7 1.6 - - - +
50X ASN* 5.4 4.5 - - - +
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Residues in contact with ALA 53 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42U ILE 5.4 8.3 - - - +
43U LYS* 6.4 0.7 - - - -
44U ALA 5.7 3.1 - - - +
49U ALA 2.9 18.5 + - - +
50U ARG* 3.3 8.0 + - - +
52U LYS* 1.3 78.2 - - - +
54U LYS* 1.3 59.4 + - - +
57U ASP* 2.9 26.1 - - - +
60U ASN* 3.7 8.8 + - - -
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Residues in contact with LYS 54 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50U ARG 2.9 17.1 + - - +
51U TYR* 4.1 6.5 - - - +
53U ALA* 1.3 73.5 - - - +
55U TYR* 1.3 97.2 + - + +
60U ASN* 2.4 32.7 + - - +
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Residues in contact with TYR 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TYR* 2.9 53.3 + + - +
54U LYS* 1.3 120.5 + - + +
56U PHE* 1.3 71.2 + - + +
57U ASP 3.6 2.5 - - - -
60U ASN* 4.0 4.6 - - + +
61U ALA 3.6 20.6 + - - -
62U SER 4.7 3.6 + - - +
64U LYS* 4.6 21.1 - - - -
65U PRO* 3.5 28.2 - - + +
68U HIS* 3.2 36.9 + + - -
58X TRP* 3.8 4.0 + - - -
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Residues in contact with PHE 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TYR* 3.6 25.4 - + - -
52U LYS* 2.6 34.8 + - + +
55U TYR* 1.3 77.9 - - + +
57U ASP* 1.3 63.3 + - - +
65U PRO* 3.6 38.1 - - + -
42X SER* 5.2 2.2 - - - -
46X LEU* 3.2 66.5 - - + +
47X THR* 3.8 11.4 - - - +
49X ASN* 4.2 5.0 + - - +
58X TRP* 3.6 36.8 - + + -
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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