Contacts of the strand formed by residues 199 - 205 (chain D) in PDB entry 3D87
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 GLU 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D HIS* 4.7 4.3 - - + -
91D SER* 2.3 53.8 + - - +
93D ASP* 3.0 24.4 + - - +
94D ILE* 3.0 25.0 + - + +
192D ALA* 2.7 34.9 + - + +
197D LYS* 3.3 6.4 - - - +
198D TYR* 1.3 88.8 - - - +
200D GLN* 1.3 61.5 + - - +
201D TYR* 2.6 30.6 + - + -
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Residues in contact with GLN 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D HIS* 4.9 7.6 + - + +
90D TRP* 6.3 0.2 - - - +
91D SER 5.3 1.6 + - - +
92D THR* 5.3 2.3 - - - +
189D MET* 3.8 22.4 - - - +
190D VAL 3.3 9.2 - - - +
191D ASP* 3.1 22.6 + - - -
198D TYR* 3.6 16.0 + - + +
199D GLU* 1.3 76.9 - - - +
201D TYR* 1.3 80.7 + - - +
202D THR* 3.3 23.6 + - + +
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Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D SER 4.9 0.2 - - - -
92D THR* 3.0 47.7 - - + -
94D ILE* 4.1 0.2 - - + -
95D LEU* 3.1 36.1 + - + -
106D PHE* 3.7 30.3 - + + -
107D LEU* 4.1 12.1 - - + -
189D MET* 3.4 2.4 - - - -
190D VAL* 2.8 50.4 + - + +
192D ALA* 4.0 22.2 - - + -
199D GLU* 2.6 37.6 + - + -
200D GLN* 1.3 80.9 - - - +
202D THR* 1.3 64.4 - - - +
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Residues in contact with THR 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 6.1 0.7 - - - +
107D LEU* 3.9 7.9 + - - +
187D GLU* 5.4 1.1 - - - -
188D VAL 3.0 12.1 - - - +
189D MET* 4.2 11.0 - - + -
200D GLN* 3.3 30.5 + - + +
201D TYR* 1.3 81.8 - - - +
203D SER* 1.3 64.7 + - - +
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Residues in contact with SER 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.9 30.6 + - - -
109D CYS* 4.2 4.7 - - - -
186D ILE 3.6 0.5 - - - +
187D GLU* 3.5 7.0 - - - +
188D VAL* 2.8 31.7 + - - -
202D THR* 1.3 78.6 - - - +
204D SER* 1.3 65.1 + - - +
205D PHE* 3.6 24.0 - - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 6.2 4.3 - - - -
185D PRO* 4.2 11.7 - - - +
186D ILE 3.2 5.2 - - - -
187D GLU* 2.8 30.7 + - - -
203D SER* 1.3 74.2 + - - +
205D PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D CYS* 3.1 31.0 - - + -
118D PHE* 3.5 28.7 - + - -
185D PRO* 4.0 4.9 - - - +
186D ILE* 3.0 58.8 + - + +
188D VAL* 3.8 10.8 - - + -
203D SER* 3.6 21.3 - - - -
204D SER* 1.3 74.7 - - - +
206D PHE* 1.3 61.0 + - - +
207D ILE* 4.0 14.8 - - + -
209D ASP* 5.3 4.0 - - + -
210D ILE* 3.5 35.9 - - + -
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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