Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 2CGA
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 PRO 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TRP* 4.4 14.1 - - + +
30B GLN* 3.6 31.9 - - - +
44B GLY 4.4 2.2 - - - +
45B SER* 3.7 22.2 - - - +
137B VAL 4.5 0.2 - - - -
138B THR* 2.8 30.9 + - - -
139B THR* 3.7 16.1 + - - +
197B GLY* 1.4 85.3 - - - +
199B LEU* 1.3 59.0 + - - +
200B VAL* 4.1 13.9 - - + -
209B LEU* 3.8 11.7 - - + -
211B GLY 3.9 4.0 - - - +
213B VAL* 5.2 1.6 - - - -
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Residues in contact with LEU 199 (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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136B CYS* 4.4 7.2 - - + -
137B VAL 3.5 17.7 - - - +
138B THR* 4.0 7.2 - - - -
160B LEU* 3.8 24.7 - - + -
162B LEU* 3.9 25.8 - - + -
181B ILE* 4.8 3.6 - - + -
183B ALA* 4.1 9.2 - - + -
198B PRO* 1.3 72.8 - - - +
200B VAL* 1.3 60.4 + - - +
209B LEU* 4.0 0.7 - - - -
210B VAL* 3.1 30.6 + - + -
211B GLY* 3.1 29.1 + - - +
228B TYR* 3.7 36.6 - - + -
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 4.3 12.1 - - + -
29B TRP* 4.1 7.9 - - + +
121B VAL* 3.7 29.4 - - + -
136B CYS* 3.2 3.8 - - - +
137B VAL* 2.8 51.4 + - + +
139B THR* 6.1 1.3 - - + -
198B PRO* 4.1 11.4 - - + -
199B LEU* 1.3 78.3 - - - +
201B CYS* 1.3 62.9 + - - +
207B TRP* 3.4 31.6 - - + -
208B THR 3.3 9.6 - - - +
209B LEU* 4.0 13.7 - - + -
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Residues in contact with CYS 201 (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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130B PHE* 3.8 22.8 - - + -
134B THR* 4.9 4.0 - - + -
135B THR 5.1 0.9 - - - +
136B CYS* 2.0 49.1 - - - +
162B LEU* 4.2 5.4 - - - -
199B LEU* 5.4 0.4 - - - -
200B VAL* 1.3 74.9 - - - +
202B LYS* 1.3 59.4 + - - +
203B LYS* 4.5 0.2 - - - +
207B TRP* 3.9 3.1 - - - -
208B THR* 2.7 46.8 + - - +
210B VAL* 3.7 28.7 - - + -
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Residues in contact with LYS 202 (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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7B GLN* 5.0 9.5 + - - +
130B PHE* 5.2 1.6 - - - -
134B THR* 6.1 1.2 - - - +
135B THR 5.5 2.4 + - - -
201B CYS* 1.3 73.9 - - - +
203B LYS* 1.3 58.4 + - - +
204B ASN 4.2 0.7 - - - -
205B GLY* 3.6 31.7 + - - -
206B ALA 3.3 9.4 - - - +
207B TRP* 3.8 52.0 - - + +
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Residues in contact with LYS 203 (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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128B ASP* 4.6 15.4 - - - +
129B ASP 3.1 32.5 + - - +
130B PHE* 3.2 33.9 - - + -
201B CYS 3.6 0.2 + - - -
202B LYS* 1.3 73.0 - - - +
204B ASN* 1.3 82.2 + - - +
205B GLY 4.2 0.2 - - - +
206B ALA* 2.9 21.6 + - - +
208B THR* 3.4 21.5 - - + +
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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