Contacts of the strand formed by residues 198 - 205 (chain D) in PDB entry 4YP8
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 GLY 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D GLU* 3.6 1.6 - - - +
195D GLY* 2.6 35.5 + - - -
196D GLY 3.4 4.1 + - - -
197D PHE* 1.3 78.6 - - - +
199D VAL* 1.3 58.6 + - - -
200D VAL* 5.3 1.1 - - - +
213D LYS* 4.9 8.3 - - - -
214D LYS 3.3 13.9 - - - -
215D LEU* 4.1 0.4 - - - -
216D ALA* 3.6 15.3 - - - +
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D GLU* 5.3 0.4 - - - +
191D LYS* 3.6 31.6 - - + +
193D GLY 3.5 9.4 - - - +
194D GLU* 3.9 20.4 - - + +
198D GLY* 1.3 76.2 - - - -
200D VAL* 1.3 64.2 + - - +
201D TYR* 3.4 37.4 - - + +
212D VAL 3.6 2.3 - - - +
213D LYS* 3.4 1.1 - - - -
214D LYS* 2.8 41.4 + - + +
216D ALA* 5.4 6.5 - - + -
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LYS 4.0 0.2 - - - -
192D MET* 2.9 39.3 + - + +
193D GLY 2.8 14.0 + - - +
195D GLY* 5.8 0.4 - - - -
198D GLY 5.3 1.3 - - - +
199D VAL* 1.3 76.4 - - - +
201D TYR* 1.3 56.4 - - - +
211D ALA* 4.1 8.1 - - + -
212D VAL 3.6 8.5 - - - +
213D LYS* 3.9 16.2 - - + +
501D 4GF 3.4 86.4 - - + +
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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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177D THR* 4.1 17.9 - - + -
180D PHE* 3.5 47.6 - + + -
181D ASP 4.0 2.2 - - - -
182D GLU* 2.6 38.5 + - - -
190D ASN* 3.2 19.7 - - + +
191D LYS* 3.8 17.7 - - + -
192D MET* 3.3 14.8 - - - +
199D VAL* 3.4 36.6 - - + +
200D VAL* 1.3 72.2 - - - +
202D LYS* 1.3 59.8 + - - +
211D ALA* 3.3 1.0 - - - -
212D VAL* 2.9 41.8 + - - +
214D LYS* 3.7 18.3 + - + -
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Residues in contact with LYS 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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202C LYS* 5.4 7.7 - - - +
501C 4GF 6.4 0.2 - - - +
177D THR* 3.7 6.7 - - - -
185D ILE* 3.9 28.8 - - + +
190D ASN* 2.7 48.8 + - - +
192D MET* 3.8 11.0 - - - -
201D TYR* 1.3 71.6 - - - +
203D GLY* 1.3 58.4 + - - +
204D TYR* 3.3 28.4 + - + +
209D THR* 3.7 24.9 - - + -
210D VAL 3.6 3.4 - - - +
264D TYR* 3.3 34.5 + - + +
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Residues in contact with GLY 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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176D VAL* 3.3 16.4 - - - -
177D THR* 4.3 6.5 - - - +
201D TYR 4.0 0.6 + - - -
202D LYS* 1.3 74.1 - - - +
204D TYR* 1.4 72.4 + - - -
209D THR* 3.5 6.4 - - - +
210D VAL* 2.9 43.2 + - - +
212D VAL* 4.7 0.6 - - - +
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Residues in contact with TYR 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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185C ILE 3.3 26.9 + - - -
186C SER* 3.1 22.4 - - - -
187C VAL* 3.6 18.8 - - - +
188C GLY* 3.6 18.8 - - - -
176D VAL* 3.3 33.2 + - - +
190D ASN* 4.9 10.1 - - - -
202D LYS* 3.3 34.1 + - + +
203D GLY* 1.4 80.6 - - - -
205D VAL* 1.3 61.6 + - - +
206D ASN 4.0 6.1 + - - +
208D THR 3.5 3.6 - - - +
209D THR* 3.4 25.4 - - + -
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Residues in contact with VAL 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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168D PHE* 3.9 35.9 - - + -
173D LEU* 5.1 0.2 - - + -
176D VAL* 3.9 20.9 - - + -
203D GLY 4.3 0.2 - - - -
204D TYR* 1.3 73.3 - - - +
206D ASN* 1.4 71.1 + - - +
208D THR* 2.9 38.4 + - - +
210D VAL* 3.8 28.9 - - + -
261D VAL* 5.0 1.3 - - + -
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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