Contacts of the strand formed by residues 234 - 239 (chain D) in PDB entry 3VD1
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 GLN 234 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D MET* 4.0 4.9 - - - +
179D PRO* 3.7 21.1 - - - +
190D VAL* 4.6 3.3 - - + +
191D VAL 5.2 4.5 - - - +
192D LYS* 3.2 45.5 - - + +
210D PRO* 6.2 0.2 - - - +
212D SER* 3.2 27.5 + - - +
213D HIS* 3.3 36.7 + - + +
214D LEU 6.0 0.4 - - - +
226D VAL 2.9 5.4 - - - +
227D ASP* 2.7 25.3 + - + +
232D GLY 5.2 1.3 - - - +
233D ARG* 1.3 76.7 - - - +
235D SER* 1.3 62.0 + - - +
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Residues in contact with SER 235 (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 ARG* 3.4 24.6 + - - -
177D ALA 3.2 17.5 - - - -
178D MET* 3.4 20.5 - - - +
179D PRO* 5.2 0.9 - - - -
213D HIS* 3.6 9.4 + - - -
215D ILE* 6.1 1.3 - - - -
224D GLN 3.9 0.2 - - - +
225D TYR* 3.5 3.3 - - - -
226D VAL* 2.6 53.0 + - - +
233D ARG 5.1 0.6 + - - -
234D GLN* 1.3 76.2 - - - +
236D VAL* 1.3 59.7 + - - +
237D VAL* 4.1 0.9 - - - +
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Residues in contact with VAL 236 (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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175D ILE 3.7 0.2 - - - +
176D ARG* 3.1 2.1 - - - -
177D ALA* 2.9 36.6 + - + -
215D ILE* 3.6 33.1 - - + +
217D VAL* 3.3 35.8 - - + +
223D SER* 4.4 3.8 - - - -
224D GLN 3.7 4.5 - - - +
225D TYR* 3.5 35.7 - - + -
235D SER* 1.3 74.5 - - - +
237D VAL* 1.3 70.4 + - - +
254D TYR* 3.8 1.8 + - + -
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Residues in contact with VAL 237 (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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174D ALA* 5.0 9.0 - - + -
175D ILE 2.9 11.9 - - - +
176D ARG* 3.2 50.3 - - + +
217D VAL* 5.8 0.2 - - - -
222D LEU 4.2 0.5 - - - +
223D SER* 3.5 0.5 - - - -
224D GLN* 3.0 47.9 + - + +
226D VAL* 4.5 7.0 - - + -
235D SER* 4.1 4.0 - - - +
236D VAL* 1.3 76.9 - - - +
238D VAL* 1.3 76.2 + - - +
239D PRO* 5.5 0.4 - - + -
278D GLU* 5.3 0.4 - - - +
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Residues in contact with VAL 238 (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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174D ALA* 3.7 4.3 - - - -
175D ILE* 2.9 38.6 + - + +
217D VAL* 4.3 16.6 - - + -
220D ASN* 4.2 18.8 - - - +
223D SER* 3.5 28.9 - - - +
237D VAL* 1.3 86.0 - - - +
239D PRO* 1.3 82.3 - - + +
240D TYR 3.2 0.2 + - - -
252D ILE* 4.6 22.2 - - + -
254D TYR* 5.4 1.8 - - - +
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Residues in contact with PRO 239 (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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114A PHE* 6.1 0.2 - - - -
173D THR 4.0 2.9 - - - +
174D ALA* 3.6 11.4 - - + -
220D ASN* 5.0 3.5 + - - +
222D LEU* 3.8 37.9 - - + +
237D VAL* 6.0 0.4 - - + -
238D VAL* 1.3 93.3 - - + +
240D TYR* 1.3 69.0 + - - +
241D GLU* 3.6 18.5 + - + +
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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