Contacts of the strand formed by residues 205 - 211 (chain A) in PDB entry 5GGR
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLY* 4.1 6.6 - - - -
119A PRO* 4.1 25.8 - - + +
198A VAL* 5.9 0.9 - - + -
199A ASN* 2.9 8.6 + - - +
200A HIS* 2.6 38.1 + - - -
203A SER* 2.9 25.7 + - - -
204A ASN* 1.3 77.6 + - - +
206A LYS* 1.3 63.9 + - - +
207A VAL* 3.8 22.9 - - + -
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Residues in contact with LYS 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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197A ASN* 5.0 11.4 + - - +
198A VAL 3.1 12.7 + - - +
199A ASN* 3.7 26.7 - - - +
204A ASN 4.3 0.2 - - - -
205A THR* 1.3 75.8 - - - +
207A VAL* 1.3 66.9 + - - +
208A ASP* 4.9 17.1 + - - +
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Residues in contact with VAL 207 (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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119A PRO 5.1 3.4 - - - +
121A VAL* 4.0 36.3 - - + -
196A CYS 3.7 0.3 - - - +
197A ASN* 3.5 0.3 - - - -
198A VAL* 2.6 44.5 + - + +
205A THR* 3.8 20.2 - - + -
206A LYS* 1.3 80.3 - - - +
208A ASP* 1.3 79.3 + - - +
209A LYS* 4.3 10.5 + - + +
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Residues in contact with ASP 208 (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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195A ILE* 3.5 24.9 - - + +
196A CYS 2.9 4.3 - - - +
197A ASN* 3.3 29.4 - - - +
198A VAL 4.2 0.2 + - - -
206A LYS* 4.9 15.5 - - - +
207A VAL* 1.3 90.2 + - - +
209A LYS* 1.3 62.3 + - - +
210A LYS 4.0 1.0 + - - -
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Residues in contact with LYS 209 (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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121A VAL* 3.5 43.9 + - + +
123A PRO* 4.3 21.3 - - + -
140A CYS* 4.7 4.3 - - - -
195A ILE* 3.1 4.3 - - - -
196A CYS* 2.6 47.0 + - + +
207A VAL* 4.1 10.7 - - + +
208A ASP* 1.3 77.0 - - - +
210A LYS* 1.3 64.2 + - - +
211A VAL* 3.6 1.7 + - - +
123B GLU* 3.4 35.1 + - - -
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Residues in contact with LYS 210 (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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123A PRO* 5.1 3.5 - - - +
193A THR* 3.8 29.6 - - + -
194A TYR 3.6 3.8 - - - +
195A ILE* 4.3 10.3 - - + +
208A ASP 4.0 1.8 + - - +
209A LYS* 1.3 76.5 - - - +
211A VAL* 1.3 61.3 + - - +
212A GLU* 3.4 32.6 + - + +
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Residues in contact with VAL 211 (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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123A PRO* 4.3 12.8 - - + -
124A LEU 3.7 29.2 - - - +
125A ALA* 5.1 0.2 - - - -
126A PRO* 4.7 5.1 - - + +
138A LEU* 3.9 25.3 - - + +
139A GLY 4.0 4.5 - - - +
140A CYS* 3.2 31.2 - - - -
154A TRP* 4.2 9.6 - - + -
194A TYR* 2.9 31.0 + - - +
209A LYS 3.9 9.4 - - - +
210A LYS* 1.3 73.8 - - - +
212A GLU* 1.3 68.1 + - - +
213A PRO* 4.5 1.8 - - - +
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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