Contacts of the strand formed by residues 27 - 31 (chain G) in PDB entry 1DM0
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 LYS 27 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G CYS* 4.3 4.2 + - - -
5G VAL* 3.9 15.3 - - + -
22G VAL 3.9 0.2 - - - +
23G LYS* 3.0 17.7 - - - +
24G VAL 3.2 23.0 + - - +
25G GLY 3.0 1.0 - - - -
26G ASP* 1.3 109.1 + - - +
28G GLU* 1.3 59.5 + - - +
29G LEU* 3.6 20.8 - - + +
57G CYS* 4.0 17.2 + - - -
58G HIS* 3.5 42.4 - - - +
59G ASN* 3.9 6.5 - - - +
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Residues in contact with GLU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G TYR* 3.4 27.8 + - - +
13G LYS* 5.2 5.7 - - - +
21G THR* 4.1 21.5 - - + +
22G VAL 3.5 5.6 - - - +
23G LYS* 4.3 7.1 - - + +
26G ASP 5.0 0.4 - - - +
27G LYS* 1.3 75.0 - - - +
29G LEU* 1.3 58.8 + - - +
59G ASN* 3.5 28.4 + - - +
60G GLY* 2.9 26.3 + - - +
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Residues in contact with LEU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G CYS* 4.3 4.3 - - - -
5G VAL* 3.6 31.0 - - + -
21G THR* 3.5 4.0 - - - +
22G VAL* 3.1 31.4 + - + +
24G VAL* 5.3 0.4 - - + +
27G LYS* 3.6 15.5 - - + +
28G GLU* 1.3 76.2 - - - +
30G PHE* 1.3 63.4 + - - +
52G ILE* 4.1 18.4 - - + -
54G THR* 4.1 12.6 - - + -
56G ALA 3.3 26.2 - - - +
58G HIS 3.6 15.9 - - - +
61G GLY 3.1 17.5 - - - +
62G GLY 5.3 0.4 - - - -
63G PHE* 3.9 13.7 - - + -
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Residues in contact with PHE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASN* 4.7 1.3 - - - +
19G THR* 3.8 26.0 - - + -
20G PHE 3.4 9.4 - - - +
21G THR* 3.5 19.7 - - - +
29G LEU* 1.3 76.8 - - - +
31G THR* 1.3 75.8 + - - +
32G ASN* 4.4 11.0 - - + -
60G GLY* 3.5 27.8 - - - -
61G GLY 3.0 8.8 + - - -
62G GLY* 3.1 20.1 - - - -
63G PHE* 2.8 29.7 + - - -
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Residues in contact with THR 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G THR* 3.4 2.8 - - - -
20G PHE* 2.9 54.0 + - + +
30G PHE* 1.3 81.2 - - - +
32G ASN* 1.3 62.1 + - - +
33G ARG* 3.2 31.5 + - - +
34G TRP* 5.8 0.3 - - - -
36G LEU* 4.0 9.2 - - + +
37G GLN* 5.3 0.7 + - - -
40G LEU* 4.4 11.9 - - + -
63G PHE* 3.1 41.8 + - + +
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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