Contacts of the strand formed by residues 55 - 60 (chain B) in PDB entry 1CD9
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 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B SER 4.0 7.6 - - - +
43B PHE* 4.1 6.4 - - - +
53B GLY 3.8 2.0 + - - -
54B ASP* 1.3 75.4 + - - +
56B ILE* 1.3 76.1 + - - +
57B PRO* 3.9 6.5 - - + +
58B ASP* 5.1 6.3 - - - +
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Residues in contact with ILE 56 (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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42B SER* 3.1 32.8 + - - +
43B PHE 4.0 2.5 - - - -
44B ARG* 3.9 39.0 - - + +
54B ASP 4.0 2.2 - - - +
55B THR* 1.3 83.0 - - - +
57B PRO* 1.3 84.2 - - + +
58B ASP* 3.3 5.9 + - - +
70B ILE* 4.4 11.0 - - + -
74B ASN* 3.6 31.6 - - + +
75B LEU* 5.2 1.8 - - + -
76B LEU 5.9 0.2 - - - +
81B MET* 3.5 32.8 - - + -
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Residues in contact with PRO 57 (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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40B LEU 4.8 0.5 - - - +
42B SER* 5.2 2.1 + - - -
55B THR* 4.0 6.7 - - + +
56B ILE* 1.3 98.6 - - + +
58B ASP* 1.3 70.2 + - - +
59B CYS* 3.5 4.2 + - - +
70B ILE* 5.7 4.0 - - - +
74B ASN* 3.8 29.7 - - + +
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Residues in contact with ASP 58 (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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39B ILE* 3.6 20.9 - - + +
40B LEU 3.6 5.6 - - - -
41B LYS* 3.4 42.8 + - - +
42B SER 5.0 0.3 + - - -
55B THR* 5.1 5.9 - - - +
56B ILE 4.1 6.7 - - - +
57B PRO* 1.3 77.7 - - - +
59B CYS* 1.3 60.2 + - - +
60B VAL* 3.9 8.5 + - + +
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Residues in contact with CYS 59 (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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39B ILE* 3.5 0.9 - - - -
40B LEU* 2.7 50.2 + - + +
57B PRO 3.5 3.1 + - - +
58B ASP* 1.3 73.8 - - - +
60B VAL* 1.3 58.1 + - - +
61B ALA 3.9 0.3 + - - -
68B CYS* 2.1 48.2 - - - +
69B SER 3.1 29.8 - - - -
70B ILE* 4.6 12.6 - - + -
71B PRO* 5.8 0.7 - - - -
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Residues in contact with VAL 60 (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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38B PHE 3.9 4.7 - - - +
39B ILE* 3.7 30.7 - - + -
58B ASP* 3.9 9.0 + - + +
59B CYS* 1.3 73.7 - - - +
61B ALA* 1.3 64.7 + - - +
62B LYS* 3.8 2.9 + - - +
68B CYS* 3.6 9.2 - - - -
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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