Contacts of the strand formed by residues 200 - 203 (chain G) in PDB entry 5U07
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 GLU 200 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F THR 2.8 27.2 - - - +
28F VAL* 3.5 19.6 - - - +
29F VAL* 4.4 10.9 + - + -
37F ARG* 4.5 2.6 + - - +
14G TYR* 2.8 39.2 - - + +
198G THR 3.4 5.3 + - - +
199G VAL* 1.3 71.1 - - - +
201G VAL* 1.3 66.6 + - - +
202G ASP* 3.4 1.7 + - - +
225G GLN* 4.3 1.1 - - - -
226G PHE* 2.9 42.8 + - - +
227G SER* 4.2 10.3 - - - +
228G ALA 4.8 0.3 + - - -
43J ARG* 3.9 8.1 - - - +
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Residues in contact with VAL 201 (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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20F ASP* 5.6 1.7 - - - +
37F ARG* 4.6 4.0 + - - -
199G VAL* 3.7 2.9 + - + +
200G GLU* 1.3 73.6 - - - +
202G ASP* 1.3 61.2 + - - +
203G PHE* 4.0 2.7 + - + +
223G ALA* 3.6 31.9 - - + +
225G GLN* 4.0 23.1 - - + +
33J ARG 5.6 4.9 - - - +
37J LEU* 4.5 22.7 - - + -
43J ARG* 4.1 20.3 + - - +
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Residues in contact with ASP 202 (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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20F ASP* 5.9 0.4 - - - -
26F LYS* 3.8 10.2 + - - +
37F ARG* 2.4 38.1 + - - +
41F GLN* 3.7 19.6 + - - +
190F HIS* 5.1 1.6 - - - -
14G TYR* 3.0 22.0 - - - +
200G GLU 3.4 1.1 + - - +
201G VAL* 1.3 72.1 - - - +
203G PHE* 1.3 62.8 + - - +
204G PHE* 3.3 8.3 + - - +
223G ALA* 4.1 1.6 - - - -
224G GLY 2.9 42.1 + - - +
226G PHE* 3.5 13.4 - - + -
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Residues in contact with PHE 203 (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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19F ARG 5.0 0.2 - - - -
20F ASP* 4.5 16.7 + - + +
21F ASP* 4.3 34.1 - - + +
26F LYS* 3.1 26.4 + - - +
201G VAL* 4.0 3.8 + - + +
202G ASP* 1.3 73.1 + - - +
204G PHE* 1.3 60.8 + - - +
205G THR* 3.4 22.4 - - - -
219G GLY 4.5 0.2 - - - -
220G HIS* 5.0 6.5 - + - -
221G MET 3.1 34.8 - - - -
223G ALA* 3.8 19.4 - - + +
27K C 3.7 47.8 - + - -
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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