Contacts of the helix formed by residues 53 - 58 (chain A) in PDB entry 1DWQ
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.6 2.9 - - - +
52A ASN* 1.3 79.4 - - - +
54A PHE* 1.3 59.7 + - - +
55A ASP* 3.2 14.0 + - - +
56A GLU* 3.0 29.3 + - - +
57A TYR* 3.0 26.5 + - - +
180A PHE* 3.5 16.7 - - - -
183A VAL* 3.8 19.1 - - - -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.9 13.9 - - + -
53A SER* 1.3 74.5 - - - +
55A ASP* 1.3 57.2 + - - +
57A TYR* 3.4 22.5 - + - +
58A SER* 2.8 32.0 + - - -
81A CSA 3.8 19.7 - - + -
84A LEU* 3.5 27.6 - - + -
85A ASN* 3.5 25.4 - - - -
88A ILE* 3.5 16.8 - - + -
178A SER 3.9 14.1 - - - -
179A LEU* 3.6 23.3 - - + -
180A PHE* 3.6 17.5 - + + +
183A VAL* 5.1 1.2 - - - +
184A LEU* 3.8 28.7 - - + +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 3.4 10.7 + - - +
54A PHE* 1.3 76.9 + - - +
56A GLU* 1.3 64.2 + - + +
58A SER* 3.1 14.2 + - - -
59A GLU* 3.5 8.7 + - - +
62A LEU* 4.5 6.4 - - - +
88A ILE* 3.2 25.2 - - - +
92A ARG* 3.2 13.7 + - - +
184A LEU* 5.0 0.7 - - - +
187A ARG* 3.0 47.0 + - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 4.0 6.2 - - - +
46A ARG* 4.9 1.6 + - - -
50A GLN 4.1 2.9 - - - +
51A ILE* 3.8 15.3 - - + +
52A ASN* 2.9 48.7 + - - +
53A SER* 3.0 20.5 + - - +
55A ASP* 1.3 75.0 - - + +
57A TYR* 1.3 62.6 + - - +
59A GLU* 3.2 22.4 + - - +
139A ILE* 4.9 5.0 - - - +
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS* 3.2 23.7 + - - -
11A THR 3.7 0.9 - - - -
12A ILE* 3.5 32.9 + - + -
13A CYS 5.6 0.2 - - - -
38A MET* 3.4 17.8 - - + +
39A ALA* 3.0 47.2 + - + -
41A SER* 3.3 20.0 - - - -
48A ILE* 4.9 10.1 - - + -
51A ILE* 3.5 7.3 - - + +
53A SER 3.0 13.3 + - - +
54A PHE* 3.4 35.9 - + - +
55A ASP 3.2 0.2 - - - -
56A GLU* 1.3 76.3 - - - +
58A SER* 1.3 58.1 + - - +
59A GLU 3.4 1.0 + - - -
60A PRO* 3.6 0.7 - - - +
85A ASN* 3.7 29.8 - - - -
178A SER 5.6 0.9 - - - -
180A PHE* 4.2 12.6 - + + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 4.1 5.4 - - - -
54A PHE 2.8 15.2 + - - -
55A ASP 3.1 9.8 + - - -
57A TYR* 1.3 74.1 - - - +
59A GLU* 1.3 65.3 + - - +
60A PRO* 3.4 1.6 - - - -
61A LEU* 2.9 19.0 + - - +
62A LEU* 3.3 14.2 + - - +
85A ASN* 2.8 31.8 + - - -
88A ILE* 3.5 27.1 - - - +
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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