Contacts of the strand formed by residues 203 - 208 (chain G) in PDB entry 1ZMD
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 ASP 203 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179G GLU 3.0 19.9 + - - +
180G LYS* 3.3 24.4 - - + +
181G MET 2.8 31.5 + - - +
198G GLN* 5.8 0.2 - - - -
201G GLY 3.9 0.2 + - - -
202G ALA* 1.3 70.9 - - - +
204G VAL* 1.3 59.6 + - - +
205G THR* 4.2 4.2 + - - -
236G LYS* 3.5 30.2 + - - +
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Residues in contact with VAL 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G MET* 3.3 30.7 - - + +
183G VAL* 4.1 6.1 - - + -
194G GLY* 3.6 22.2 - - - +
198G GLN* 3.8 29.0 - - + +
202G ALA* 3.6 12.0 + - + +
203G ASP* 1.3 78.0 + - - +
205G THR* 1.3 69.0 + - - +
234G GLY 4.3 1.6 + - - +
235G PHE* 3.8 29.3 - - + -
236G LYS* 3.1 29.9 + - - +
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Residues in contact with THR 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G LYS* 6.0 1.7 - - - -
181G MET 3.0 8.8 + - - -
182G VAL* 3.2 16.2 - - + +
183G VAL* 2.8 30.4 + - - +
203G ASP* 4.3 7.4 + - - -
204G VAL* 1.3 80.2 + - - +
206G ALA* 1.3 63.5 + - - +
207G VAL* 4.4 7.2 - - + -
236G LYS* 3.3 26.4 - - + +
237G PHE 4.7 0.2 - - - +
238G LYS* 4.4 28.3 - - + +
269G ILE* 5.6 2.2 - - + -
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Residues in contact with ALA 206 (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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183G VAL* 3.3 19.3 - - + +
185G GLY 4.2 11.0 - - - +
186G ALA* 4.3 5.2 - - + -
190G GLY 5.5 0.4 - - - +
205G THR* 1.3 72.1 - - - +
207G VAL* 1.3 61.7 + - - +
208G GLU* 3.9 1.4 + - - +
235G PHE* 3.6 25.0 - - + -
236G LYS 3.0 6.7 + - - -
237G PHE* 3.5 20.3 - - + +
238G LYS 2.9 24.6 + - - -
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Residues in contact with VAL 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G VAL* 4.3 10.5 - - + -
183G VAL 2.7 14.6 + - - +
184G ILE* 3.7 0.7 - - - -
185G GLY* 2.7 28.7 + - - -
205G THR* 4.4 6.3 - - + -
206G ALA* 1.3 75.3 - - - +
208G GLU* 1.3 55.9 + - - +
238G LYS* 3.5 14.1 - - + +
241G THR* 3.4 43.1 - - + +
243G VAL* 3.6 25.4 - - + -
258G ILE* 4.3 2.0 - - + -
269G ILE* 4.1 26.2 - - + -
481G NAI 3.2 8.0 - - - -
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Residues in contact with GLU 208 (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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186G ALA* 2.7 42.3 + - + +
206G ALA 3.9 0.8 + - - +
207G VAL* 1.3 73.2 - - - +
209G PHE* 1.3 62.5 + - - +
210G LEU* 3.1 32.4 + - - +
212G HIS 3.6 21.5 - - - +
238G LYS 3.1 5.9 + - - -
239G LEU* 3.1 13.4 - - + -
240G ASN 2.8 23.4 + - - -
241G THR 3.0 8.1 + - - -
481G NAI 2.5 51.5 + - - -
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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