Contacts of the strand formed by residues 208 - 213 (chain A) in PDB entry 1DST
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 VAL 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PRO* 3.6 21.5 - - + +
125A GLN* 3.3 47.1 - - + +
200A VAL* 3.4 4.9 - - - +
201A CYS 3.0 31.0 + - - +
202A GLY 3.3 8.6 - - - +
207A GLY* 1.3 82.5 - - - +
209A LEU* 1.3 70.2 + - - +
210A GLU* 3.2 4.6 + - - +
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Residues in contact with LEU 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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45A VAL* 4.2 17.7 - - + -
47A VAL* 4.4 3.6 - - + -
53A LEU* 3.8 28.9 - - + -
123A LEU* 3.8 15.6 - - + +
124A PRO* 2.9 32.2 + - - +
125A GLN* 3.0 23.6 + - - +
198A PRO* 3.4 31.0 - - + -
199A LEU 3.8 5.2 - - - +
200A VAL* 4.6 0.2 - - - +
208A VAL* 1.3 69.8 - - - +
210A GLU* 1.3 58.4 + - - +
211A GLY 3.2 25.4 - - - +
212A VAL* 4.6 1.6 - - + -
231A VAL* 3.4 17.9 - - + +
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Residues in contact with GLU 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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125A GLN* 3.2 43.1 + - - +
129A ARG 4.4 9.1 - - - +
130A VAL* 3.1 36.8 - - + +
181A MET* 4.2 12.8 - - + +
199A LEU* 3.0 13.0 + - + +
201A CYS* 3.7 23.1 - - - +
208A VAL* 3.2 8.5 + - - +
209A LEU* 1.3 75.4 - - - +
211A GLY* 1.3 59.5 + - - +
230A ARG* 3.6 10.2 + - - +
231A VAL* 3.1 24.9 + - - +
232A ALA* 4.7 3.8 - - - +
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Residues in contact with GLY 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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181A MET* 4.4 8.7 - - - -
198A PRO 3.7 0.2 - - - -
199A LEU* 2.9 38.7 + - - +
209A LEU* 3.2 11.2 - - - +
210A GLU* 1.3 79.4 - - - +
212A VAL* 1.3 64.0 + - - -
228A TYR* 4.6 2.7 - - - -
229A THR 3.0 14.6 - - - -
231A VAL* 4.5 1.3 - - - -
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Residues in contact with VAL 212 (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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45A VAL* 5.5 2.0 - - + -
53A LEU* 3.7 19.7 - - + +
54A SER* 4.1 10.3 - - - -
55A ALA* 4.5 1.6 - - + +
102A ASP 5.1 0.4 - - - +
103A LEU* 3.7 24.7 - - + -
196A GLY* 3.6 33.0 - - - +
197A GLY 3.5 3.8 - - - +
209A LEU* 4.6 4.3 - - + -
211A GLY* 1.3 79.2 - - - +
213A VAL* 1.3 73.3 + - - +
214A SER* 3.1 1.2 + - - -
228A TYR* 3.4 3.6 - - - +
229A THR* 2.9 30.9 + - - +
231A VAL* 3.7 23.6 - - + -
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Residues in contact with VAL 213 (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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55A ALA* 3.9 5.5 - - - +
102A ASP 5.6 0.2 - - - +
138A VAL* 3.8 26.2 - - + -
139A ALA 5.2 0.4 - - - +
190A SER* 3.6 25.4 - - - +
194A ASP* 3.2 33.9 - - + +
195A SER* 3.7 0.6 - - - +
196A GLY* 2.9 23.5 + - - +
197A GLY* 2.8 28.5 + - - +
198A PRO 4.2 1.1 - - - +
212A VAL* 1.3 74.0 - - - +
214A SER* 1.3 73.3 + - - +
215A TRP 5.0 0.4 - - - +
216A GLY* 5.2 0.9 - - - -
227A ILE 5.3 0.4 - - - +
228A TYR* 3.7 17.5 - - + -
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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