Contacts of the strand formed by residues 197 - 205 (chain A) in PDB entry 2YD7
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 GLY 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LYS* 4.0 2.7 - - - -
162A ASP* 3.5 12.3 - - - -
195A ASP 3.5 2.4 + - - -
196A GLN* 1.3 77.0 - - - +
198A LYS* 1.3 60.3 + - - -
199A TYR* 3.5 9.0 - - - -
216A ASN* 3.4 7.7 - - - +
217A LEU 2.9 30.8 + - - +
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Residues in contact with LYS 198 (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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160A PHE 3.7 1.2 - - - +
161A LYS* 3.3 3.2 - - - +
162A ASP* 2.7 48.3 + - - +
163A PHE* 4.8 16.8 + - + -
197A GLY* 1.3 70.6 - - - -
199A TYR* 1.3 60.0 + - - +
200A GLU* 4.1 3.6 + - + +
214A PRO* 3.5 33.4 - - + -
215A ALA 3.8 2.7 - - - +
216A ASN* 3.4 26.7 - - - +
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Residues in contact with TYR 199 (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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132A PRO* 4.0 6.1 - - - +
145A MET* 4.2 17.0 - - + -
159A TRP* 4.3 11.4 - + + -
160A PHE 3.3 6.3 - - - -
161A LYS* 3.6 35.5 - - + +
166A VAL* 4.4 5.2 - - + -
175A ILE* 5.6 2.2 - - + +
186A LEU* 3.6 32.5 - - + -
188A ILE* 3.3 20.8 - - + +
195A ASP* 2.6 33.2 + - - +
197A GLY 3.5 17.3 - - - -
198A LYS* 1.3 73.1 - - - +
200A GLU* 1.3 60.8 + - - +
214A PRO* 3.2 3.1 - - - +
215A ALA* 2.8 44.5 + - + +
217A LEU* 3.7 22.7 - - + -
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Residues in contact with GLU 200 (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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40A VAL* 4.8 1.2 - - - +
83A ARG* 2.7 46.2 + - - -
159A TRP* 3.4 10.9 - - - -
160A PHE* 2.8 48.7 + - + +
163A PHE* 3.9 12.2 + - - -
198A LYS* 5.2 3.4 - - + +
199A TYR* 1.3 76.3 - - - +
201A CYS* 1.3 58.7 + - - +
202A VAL* 3.9 1.3 + - + +
211A TYR* 3.6 21.9 - - + -
212A SER* 3.7 16.7 - - - +
214A PRO* 3.8 28.0 - - + +
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Residues in contact with CYS 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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128A ILE* 4.1 8.0 - - - +
132A PRO* 3.9 2.4 - - + +
147A CYS* 2.0 55.9 - - + -
157A ILE* 3.8 17.9 - - - -
158A THR 3.6 4.3 - - - -
159A TRP* 3.9 15.4 - - + -
200A GLU* 1.3 73.7 - - - +
202A VAL* 1.3 67.1 + - - +
210A ARG 4.0 0.3 - - - +
211A TYR* 3.6 0.7 - - - -
212A SER* 2.9 41.7 + - - +
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Residues in contact with VAL 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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156A GLU 3.4 1.7 - - - +
157A ILE* 3.2 5.0 - - - -
158A THR* 2.7 53.6 + - - +
160A PHE* 3.5 33.0 - - + -
200A GLU 4.1 4.3 - - - +
201A CYS* 1.3 81.5 - - - +
203A ALA* 1.3 59.9 + - - +
204A THR* 3.9 7.9 + - - +
209A THR* 3.4 32.1 - - + -
210A ARG 3.5 3.4 - - - +
211A TYR* 3.7 28.7 - - + +
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Residues in contact with ALA 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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126A PRO* 3.4 23.8 - - + +
128A ILE* 3.8 14.1 - - + +
149A ALA* 3.7 28.7 - - + -
155A PRO* 4.3 4.7 - - + -
156A GLU 3.4 5.8 - - - -
157A ILE* 4.6 2.2 - - + +
201A CYS 4.3 0.2 - - - -
202A VAL* 1.3 71.4 - - - +
204A THR* 1.3 61.0 + - - +
209A THR* 3.2 3.5 - - - -
210A ARG* 2.9 35.8 + - + +
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Residues in contact with THR 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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33A GLN* 5.1 4.5 + - - +
155A PRO* 3.2 5.2 - - - +
156A GLU* 2.8 49.1 + - + +
158A THR* 5.1 3.3 + - - +
202A VAL* 3.9 9.0 + - - +
203A ALA* 1.3 76.1 + - - +
205A ASN* 1.3 71.3 + - - +
208A GLY 3.3 4.3 - - - +
209A THR* 3.3 28.9 + - - +
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Residues in contact with ASN 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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124A GLY 2.9 25.7 + - - -
126A PRO* 3.4 14.4 - - - +
151A GLY* 4.1 1.8 - - - -
152A ASN 3.6 6.7 + - - +
153A PRO* 2.8 38.7 + - + +
154A ASP 4.6 1.1 - - - +
155A PRO* 4.0 5.7 - - + +
204A THR* 1.3 83.0 - - - +
206A SER* 1.3 64.7 + - - +
207A ALA* 2.9 17.7 + - - +
208A GLY* 2.9 30.2 + - - +
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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