Contacts of the strand formed by residues 207 - 212 (chain A) in PDB entry 1QS0
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 ALA 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A MSE 3.4 6.7 - - - +
130A PHE* 4.6 1.1 - - + -
191A ALA* 3.2 33.4 - - + +
194A TRP* 4.0 14.8 - - + -
195A ALA* 4.0 6.3 - - + +
206A ILE* 1.3 80.1 - - - +
208A SER* 1.3 60.5 + - - +
234A PRO 3.1 5.7 + - - -
235A VAL* 3.4 13.2 - - + -
236A ILE* 2.9 28.6 + - - +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 2.6 28.3 + - - -
123A LEU* 3.8 13.9 - - - +
127A ASP* 5.9 0.7 - - - -
128A MSE 2.9 9.3 + - - -
129A CYS* 3.2 23.1 - - - -
130A PHE* 2.7 31.2 + - - -
191A ALA* 4.9 0.2 - - - -
207A ALA* 1.3 73.0 - - - +
209A ALA* 1.3 55.1 + - - +
210A TRP* 3.1 20.6 + - - -
236A ILE* 3.8 5.4 - - - +
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.9 3.8 - - + -
188A PHE* 3.5 29.6 - - + +
191A ALA* 3.4 27.1 - - + -
207A ALA 4.0 1.0 - - - -
208A SER* 1.3 71.3 - - - +
210A TRP* 1.3 65.7 + - - +
235A VAL* 4.2 1.1 - - + +
236A ILE 2.9 12.7 + - - +
237A LEU* 4.1 8.1 - - + -
238A ASN* 2.8 35.3 + - - -
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Residues in contact with TRP 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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115A ILE* 3.5 36.6 - - + -
116A GLY* 4.1 4.0 - - - -
119A GLN* 3.6 42.4 - - + -
120A ALA 5.7 0.2 - - - -
129A CYS* 4.2 1.6 - - - +
130A PHE 3.0 24.9 + - - +
131A PRO* 3.9 7.4 - - + -
132A THR* 3.6 3.3 - - - +
135A GLN* 3.6 36.8 - - + +
138A ILE* 3.9 22.6 - - + +
187A GLN* 3.2 21.5 + - - +
188A PHE* 3.5 6.1 - - - -
208A SER* 3.1 31.5 + - - -
209A ALA* 1.3 75.3 - - - +
211A ILE* 1.3 64.6 + - - +
238A ASN* 3.4 32.1 - - + -
240A VAL* 4.1 11.7 - - + -
304A TRP* 3.9 1.6 - + - -
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Residues in contact with ILE 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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132A THR* 3.8 10.3 - - + +
135A GLN* 5.6 0.9 + - - -
185A ALA* 3.7 25.1 - - + -
187A GLN* 4.6 1.8 - - - +
188A PHE* 3.6 25.1 - - + -
210A TRP* 1.3 78.0 - - - +
212A GLY* 1.3 67.3 + - - +
215A ALA* 3.4 39.0 - - + +
216A THR* 4.0 4.7 - - + +
221A PHE* 4.1 17.3 - - + -
238A ASN 3.1 14.7 + - - +
239A VAL* 3.3 15.1 - - + -
240A VAL* 2.8 27.5 + - - +
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Residues in contact with GLY 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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132A THR* 4.5 5.7 - - - +
211A ILE* 1.3 78.8 - - - +
213A ASP* 1.3 66.2 + - - -
214A GLY 3.2 3.3 + - - -
215A ALA* 3.3 9.4 + - - +
216A THR* 3.3 16.2 + - - +
239A VAL* 4.5 0.7 - - - -
240A VAL* 3.4 13.5 - - - -
500A TPP 3.4 25.3 + - - -
501A MG 4.4 0.4 - - - -
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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