Contacts of the strand formed by residues 200 - 206 (chain A) in PDB entry 2GH1
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A GLY* 3.6 21.1 + - - +
199A VAL* 1.3 74.4 - - - +
201A ASN* 1.3 77.5 + - - +
202A ILE 3.2 3.7 + - - -
289A GLY* 3.5 1.4 - - - -
290A GLU* 2.7 44.2 + - + +
292A GLU* 3.7 45.9 + - + +
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Residues in contact with ASN 201 (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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200A LYS* 1.3 82.2 - - - +
202A ILE* 1.3 65.9 + - - +
203A GLU* 3.6 5.7 + - - +
288A PHE* 3.8 8.8 - - - +
289A GLY* 3.8 3.8 - - - -
290A GLU* 2.5 33.1 + - + +
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Residues in contact with ILE 202 (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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191A PRO* 4.0 17.7 - - + +
194A LEU* 3.7 12.8 - - + -
195A SER* 3.5 40.2 - - - +
199A VAL* 3.5 37.5 - - + +
200A LYS 4.2 0.7 - - - -
201A ASN* 1.3 75.4 - - - +
203A GLU* 1.3 65.1 + - - +
287A THR* 4.4 2.7 - - + -
288A PHE 3.4 10.1 - - - +
212B PHE* 3.9 26.8 - - + -
214B ASP* 4.3 10.3 - - - +
217B MSE 6.3 1.8 - - + -
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Residues in contact with GLU 203 (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 VAL* 3.8 4.7 - - - +
201A ASN 4.3 3.1 - - - +
202A ILE* 1.3 80.4 - - - +
204A CYS* 1.3 70.3 + - - +
205A ARG* 3.5 31.4 + - - +
287A THR* 3.5 4.2 - - - +
288A PHE* 2.9 69.5 + - + +
23B ASN* 4.5 6.8 - - - +
210B VAL 5.9 1.3 - - - +
212B PHE* 5.7 3.1 - - - -
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Residues in contact with CYS 204 (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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187A GLY 4.5 1.1 - - - -
188A MSE 4.9 2.2 - - - -
191A PRO* 4.0 19.1 - - + -
203A GLU* 1.3 79.3 - - - +
205A ARG* 1.3 77.0 + - - +
285A LYS* 4.1 20.9 - - - -
286A ILE 3.3 6.1 - - - -
287A THR* 3.4 23.3 - - - +
23B ASN* 5.4 1.2 + - - -
210B VAL* 3.1 50.5 + - + +
212B PHE* 5.8 6.1 - - + +
279B VAL* 5.2 0.2 - - + -
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Residues in contact with ARG 205 (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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26A TYR* 3.5 15.0 - - - +
29A PHE* 3.7 3.6 - - - -
30A LEU* 4.3 9.4 - - + -
34A VAL* 3.7 19.7 - - - +
203A GLU* 3.5 33.1 + - + -
204A CYS* 1.3 82.5 - - - +
206A VAL* 1.3 62.5 + - - +
285A LYS* 3.7 2.6 - - - -
286A ILE* 2.7 48.1 + - + +
288A PHE* 4.1 15.5 - - + -
23B ASN* 3.6 20.3 + - - +
25B ASP* 2.8 42.2 + - - -
208B ASP* 2.9 35.7 + - - +
210B VAL* 3.8 2.2 - - - -
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Residues in contact with VAL 206 (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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26A TYR* 3.7 3.6 + - - -
205A ARG* 1.3 74.1 - - - +
207A SER* 1.3 77.6 + - - +
208A ASP 3.1 0.5 + - - -
283A ASN* 3.3 32.1 - - - +
284A MSE 3.4 12.6 - - - +
285A LYS* 4.0 9.4 - - - -
286A ILE* 5.1 0.2 - - - -
206B VAL* 4.9 8.7 - - + -
207B SER 4.4 6.1 - - - +
208B ASP* 3.0 35.3 + - - +
209B LYS 4.2 2.9 - - - +
210B VAL* 3.3 23.6 - - + -
281B ALA* 4.0 17.3 - - + -
283B ASN* 5.2 2.2 - - - +
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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