Contacts of the helix formed by residues 55 - 64 (chain A) in PDB entry 2D8X
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 CYS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A CYS* 3.3 3.2 - - - -
37A CYS* 3.7 7.4 - - - -
39A GLU* 4.0 4.3 - - - +
41A LEU* 3.5 21.5 - - + -
44A ILE* 4.3 12.1 - - + -
45A GLY 4.6 3.8 - - - +
47A VAL* 4.4 0.4 - - - -
54A LEU* 1.3 75.3 - - - +
56A ARG* 1.3 70.0 + - - +
57A PRO* 2.8 26.5 - - + -
58A CYS* 2.9 8.7 + - - -
59A HIS* 2.9 20.7 + - - -
401A ZN 2.2 35.7 - - - -
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Residues in contact with ARG 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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44A ILE 5.8 3.8 - - - +
45A GLY 5.1 2.8 + - - -
47A VAL* 3.9 23.6 - - + +
55A CYS* 1.3 68.7 - - - +
57A PRO* 1.3 62.0 - - + +
59A HIS* 4.5 4.7 - - - -
60A ASN* 2.7 71.3 + - - +
63A LYS* 5.9 2.0 - - - +
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Residues in contact with PRO 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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39A GLU* 4.4 9.4 - - - +
44A ILE* 5.9 2.0 - - + -
55A CYS* 3.1 21.5 - - + -
56A ARG* 1.3 100.4 - - + +
58A CYS* 1.3 67.2 + - - +
60A ASN* 3.5 5.6 - - + +
61A ARG* 3.1 26.3 + - - +
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Residues in contact with CYS 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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34A CYS* 3.7 4.9 - - - -
36A LEU* 3.5 32.3 - - + -
37A CYS* 3.6 12.3 - - - -
54A LEU* 4.6 0.2 - - + -
55A CYS* 2.9 8.1 + - - +
57A PRO* 1.3 76.0 - - - +
59A HIS* 1.3 58.0 + - - +
61A ARG* 2.4 46.6 + - - +
62A GLU* 2.9 13.6 + - - +
401A ZN 2.1 36.6 - - - -
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Residues in contact with HIS 59 (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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47A VAL* 3.2 46.0 - - + +
48A LYS 5.6 0.2 - - - -
49A ASN* 3.5 23.9 + - - -
54A LEU* 4.1 22.4 - - + +
55A CYS 2.9 17.7 + - - +
56A ARG* 4.0 7.0 - - - +
58A CYS* 1.3 72.6 - - - +
60A ASN* 1.3 65.7 + - - +
62A GLU* 3.7 3.1 - - - +
63A LYS* 2.8 68.6 + - + +
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Residues in contact with ASN 60 (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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56A ARG* 2.7 71.7 + - - +
57A PRO* 3.5 6.1 - - + +
58A CYS 2.8 3.4 + - - -
59A HIS* 1.3 78.0 + - - +
61A ARG* 1.3 56.1 + - + +
63A LYS* 3.6 24.4 + - - +
64A ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 61 (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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57A PRO* 3.1 19.9 + - - +
58A CYS* 2.4 34.9 + - - +
60A ASN* 1.3 71.9 - - + +
62A GLU* 1.3 66.8 + - - +
64A ALA* 3.3 16.5 - - - +
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Residues in contact with GLU 62 (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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36A LEU* 3.5 42.6 - - + +
49A ASN* 5.1 6.7 - - - +
54A LEU* 4.9 3.6 - - + -
58A CYS* 2.9 14.5 + - - +
59A HIS* 3.7 6.7 - - - +
61A ARG* 1.3 81.7 - - - +
63A LYS* 1.3 67.2 + - - +
64A ALA 2.9 8.7 + - - +
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Residues in contact with LYS 63 (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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49A ASN* 4.6 7.3 - - - +
56A ARG* 5.9 1.6 - - - +
59A HIS* 2.8 55.9 + - + +
60A ASN* 3.6 23.1 + - - +
62A GLU* 1.3 74.2 - - - +
64A ALA* 1.3 70.9 + - - +
65A SER* 2.8 11.3 + - - -
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Residues in contact with ALA 64 (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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60A ASN 2.9 23.6 + - - +
61A ARG* 3.3 16.1 - - - +
62A GLU 2.9 7.0 + - - +
63A LYS* 1.3 78.5 - - - +
65A SER* 1.3 66.3 + - - +
66A GLY* 3.4 2.9 + - - -
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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