Contacts of the strand formed by residues 198 - 204 (chain D) in PDB entry 5EWL
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 198 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D TYR 2.9 10.2 + - - -
168D ILE* 3.6 23.7 - - + -
169D PHE* 3.1 29.2 + - - +
196D GLY 3.8 2.9 + - - +
197D TRP* 1.3 76.0 - - - +
199D LEU* 1.3 59.7 + - - +
200D GLU* 3.3 9.4 + - + +
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Residues in contact with LEU 199 (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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169D PHE* 3.4 30.4 - - + +
171D ILE* 3.7 34.8 - - + +
186D ILE* 4.9 2.5 - - + -
187D ARG* 3.8 33.1 + - + +
190D ILE* 4.6 11.2 - - + +
197D TRP 4.2 1.0 - - - -
198D GLU* 1.3 68.2 - - - +
200D GLU* 1.3 62.4 + - - +
201D GLU* 3.3 25.7 - - - +
202D VAL* 3.8 20.4 - - + -
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 3.2 24.2 - - + +
169D PHE 2.9 7.9 + - - -
170D SER* 3.6 1.1 - - - +
198D GLU* 3.8 16.2 - - + +
199D LEU* 1.3 72.2 - - - +
201D GLU* 1.3 67.9 + - + +
224D GLN* 4.3 8.9 - - + +
225D SER* 2.7 41.1 + - - +
226D PRO* 4.5 0.2 - - - +
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Residues in contact with GLU 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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170D SER* 3.2 18.3 + - - +
171D ILE 2.9 26.2 + - - -
199D LEU* 3.3 6.7 - - - +
200D GLU* 1.3 83.1 - - - +
202D VAL* 1.3 82.8 + - - +
203D LEU* 4.0 16.8 - - + +
222D LYS* 4.3 22.9 - - + +
223D LEU* 4.5 12.1 - - + -
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Residues in contact with VAL 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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171D ILE* 3.2 13.5 - - + +
173D THR* 5.6 0.7 - - - +
183D VAL* 4.0 32.1 - - + -
187D ARG* 3.6 32.5 - - - +
199D LEU* 3.8 21.1 - - + -
201D GLU* 1.3 90.0 + - - +
203D LEU* 1.3 69.1 + - - +
204D LEU 4.2 0.7 + - - -
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Residues in contact with LEU 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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171D ILE 2.9 9.1 + - - -
172D VAL* 4.1 17.0 - - + -
173D THR* 2.9 31.6 + - - +
201D GLU* 4.0 27.4 - - + +
202D VAL* 1.3 79.8 - - - +
204D LEU* 1.3 58.9 + - - +
205D LEU* 4.0 7.6 - - + -
219D GLN* 3.3 45.3 - - + +
220D LEU* 4.2 7.9 - - + +
222D LYS* 4.5 6.3 - - + -
223D LEU* 3.8 32.1 - - + -
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Residues in contact with LEU 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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173D THR* 3.4 11.0 - - - +
174D THR 3.3 31.9 - - - +
175D TYR* 3.6 39.7 - - + +
179D TYR* 3.6 28.0 - - + +
202D VAL 4.2 1.0 + - - -
203D LEU* 1.3 72.5 - - - +
205D LEU* 1.3 61.9 + - - +
206D ASP* 3.9 1.8 + - - +
219D GLN* 2.9 21.4 + - - +
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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