Contacts of the strand formed by residues 198 - 203 (chain D) in PDB entry 5YL4
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
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Residue Dist Surf HB Arom Phob DC
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163D ILE* 3.9 9.3 - - + +
164D MET 3.4 2.1 + - - +
165D ASN* 3.0 30.1 - - + +
166D THR 2.9 24.1 + - - -
196D THR* 3.6 1.2 - - - -
197D ASP* 1.3 86.0 - - + +
199D THR* 1.3 62.4 + - - +
200D TYR* 5.1 0.4 - - - -
250D LEU* 3.1 31.4 - - - +
253D LEU* 3.0 31.7 - - - +
254D ALA* 4.1 12.2 - - - -
258D VAL* 5.0 0.2 - - + -
264D HIS* 3.6 7.0 - - - -
266D PHE* 3.3 31.2 - - + -
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Residues in contact with THR 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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166D THR* 2.7 26.3 + - - +
168D SER* 3.4 23.6 - - - +
170D MET* 6.3 0.2 - - - -
192D LEU* 4.0 8.2 - - + +
196D THR* 3.2 20.4 + - - -
198D GLU* 1.3 71.1 + - - +
200D TYR* 1.3 67.0 + - - +
201D CYS* 3.4 5.3 + - - -
264D HIS* 2.9 9.5 + - - -
265D PHE* 3.4 32.0 - - + -
266D PHE* 3.0 26.0 + - - -
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Residues in contact with TYR 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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165D ASN* 3.2 34.8 - - - -
166D THR 2.9 15.3 + - - +
167D PHE* 3.6 32.6 - + + -
168D SER 3.2 21.5 + - - +
198D GLU* 5.2 0.4 - - - -
199D THR* 1.3 70.9 - - - +
201D CYS* 1.3 59.7 + - - +
202D ILE* 3.1 10.8 + - + +
232D THR* 5.9 1.3 - - + -
236D VAL* 3.9 36.5 + - + +
253D LEU* 3.4 26.5 - - + +
266D PHE* 3.7 25.6 - + + -
268D PRO* 4.4 17.0 - - + -
368D ILE* 3.6 29.5 - - + +
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Residues in contact with CYS 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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168D SER 3.9 5.8 - - - -
170D MET* 4.5 13.9 - - + -
199D THR* 4.1 6.3 - - - -
200D TYR* 1.3 67.4 - - - +
202D ILE* 1.3 61.1 + - - +
203D ASP 3.4 5.5 + - - -
265D PHE* 3.8 38.8 - - - -
266D PHE 3.1 18.7 + - - +
268D PRO* 3.2 18.9 - - - +
300D MET 3.8 3.6 - - - +
301D ALA* 3.8 4.6 - - + +
374D ILE* 4.1 20.0 - - + -
377D LEU* 4.3 13.9 - - + -
378D PHE* 4.8 5.4 - - - -
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Residues in contact with ILE 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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16D ILE* 5.3 0.4 - - + -
167D PHE* 3.7 44.9 - - + +
168D SER 3.3 4.3 + - - +
169D VAL* 3.2 25.0 - - + +
170D MET* 2.9 22.7 + - - -
200D TYR* 3.1 7.4 + - + +
201D CYS* 1.3 70.1 - - - +
203D ASP* 1.3 59.0 + - - +
207D LEU* 3.6 13.5 - - + -
229D VAL* 3.4 47.3 - - + -
232D THR* 5.1 10.3 - - + -
233D MET* 4.6 2.2 - - + -
268D PRO* 4.4 13.9 - - + -
300D MET* 4.1 7.0 - - + -
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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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170D MET* 3.6 10.3 - - - +
201D CYS 3.4 0.4 + - - -
202D ILE* 1.3 72.2 - - - +
204D ASN* 1.3 67.9 + - - +
205D GLU* 3.4 9.2 + - - -
206D ALA* 3.2 1.4 + - + -
207D LEU* 3.1 25.8 + - - +
300D MET 2.8 20.2 + - - +
301D ALA* 3.7 10.8 - - - -
302D ALA* 3.2 18.3 + - - +
377D LEU* 3.5 19.0 - - + +
380D ARG* 2.8 45.3 + - - -
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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