Contacts of the strand formed by residues 200 - 204 (chain D) in PDB entry 5E9W
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 THR 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D ASP* 3.9 7.6 + - - +
199D ILE* 1.3 73.9 + - - +
201D VAL* 1.3 65.8 + - - +
221D ASN* 4.7 4.0 + - - -
222D LYS* 3.3 19.7 - - + +
276D MET* 3.5 28.9 - - + -
277D CYS 3.4 26.0 - - - +
278D PHE* 3.7 7.1 - - + -
279D ASP* 2.7 43.5 + - - +
280D ILE 3.4 4.0 + - - -
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Residues in contact with VAL 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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188D LEU* 4.8 0.4 - - + -
199D ILE* 4.1 17.0 - - + -
200D THR* 1.3 81.3 - - - +
202D LEU* 1.3 70.5 + - - +
215D TRP* 3.6 43.7 - - + -
220D ILE* 3.8 18.4 - - + -
222D LYS 2.9 7.3 + - - -
223D LEU* 3.5 18.9 - - + +
224D VAL 2.9 26.0 + - - -
278D PHE* 3.7 6.4 - - - -
280D ILE* 3.3 21.3 - - + +
282D SER* 4.7 0.4 - - - -
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Residues in contact with LEU 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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201D VAL* 1.3 73.5 - - - +
203D ASP* 1.3 57.8 + - - +
204D LEU* 3.5 9.2 + - + -
224D VAL* 3.6 31.0 - - + +
226D THR* 4.0 18.8 - - + -
267D LEU* 3.8 17.9 - - + -
271D PHE* 4.6 0.9 - - + -
278D PHE* 3.5 35.5 - - + -
280D ILE 2.9 10.5 + - - +
281D CYS* 3.3 21.9 - - + -
282D SER 2.9 26.2 + - - -
303D ASN 3.4 25.6 - - - +
304D ALA* 4.5 0.2 - - - -
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Residues in contact with ASP 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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201D VAL 3.9 1.6 + - - -
202D LEU* 1.3 71.9 - - - +
204D LEU* 1.3 61.7 + - - +
205D GLY 4.5 1.0 - - - +
206D CYS* 3.5 29.1 + - + +
209D GLY* 6.2 0.5 - - - -
211D ASP* 3.8 18.7 + - - +
212D LEU 5.4 0.3 + - - -
215D TRP* 3.5 23.4 + - + +
223D LEU* 4.0 16.4 - - + -
224D VAL 2.8 14.4 + - - +
225D CYS* 4.7 5.5 - - - -
226D THR 3.1 28.1 + - - +
282D SER* 3.4 17.2 + - - +
284D GLN* 5.3 1.7 + - - +
501D SAH 4.6 5.1 + - - -
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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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202D LEU* 3.5 13.4 + - + -
203D ASP* 1.3 70.2 - - - +
205D GLY* 1.3 66.4 + - - +
226D THR* 3.9 10.5 - - + -
262D SER* 3.8 28.9 - - - +
267D LEU* 4.4 0.4 - - + -
281D CYS* 4.1 9.0 - - - -
282D SER 3.0 14.0 + - - +
283D CYS* 3.8 17.6 - - - -
284D GLN 4.4 0.5 + - - -
286D VAL* 3.5 31.3 - - + +
300D MET* 4.1 18.8 - - + +
303D ASN* 4.2 9.2 - - + -
304D ALA* 4.0 36.8 - - + +
501D SAH 4.6 1.6 - - + -
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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