Contacts of the strand formed by residues 207 - 211 (chain T) in PDB entry 3EXG
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 ILE 207 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206T HIS* 1.3 79.1 - - + +
208T THR* 1.3 69.3 + - - +
209T VAL* 4.4 4.7 - - + -
231T VAL* 5.0 0.7 - - + -
232T GLU 3.6 2.0 + - - +
233T CYS* 3.8 28.7 - - + -
234T GLU 3.0 24.4 + - - -
256T THR* 3.5 16.8 - - - +
258T HIS* 3.5 27.6 - - + +
260T VAL* 3.9 26.5 - - + -
323T ILE* 4.3 24.0 - - + -
326T THR* 4.2 8.3 - - + -
327T LEU* 4.3 12.3 - - + -
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Residues in contact with THR 208 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207T ILE* 1.3 72.7 - - - +
209T VAL* 1.3 63.1 + - - +
210T VAL* 3.8 15.5 - - + -
234T GLU 3.5 9.2 - - - +
236T ILE* 3.8 20.0 - - + -
249T ILE* 4.7 4.0 - - + -
252T SER* 2.3 39.9 + - - +
253T VAL* 3.6 7.4 + - - -
256T THR* 2.9 17.7 + - - +
258T HIS 2.8 17.2 + - - -
259T LEU* 3.4 5.7 - - + +
260T VAL 2.9 26.5 + - - +
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Residues in contact with VAL 209 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207T ILE* 4.4 4.9 - - + -
208T THR* 1.3 73.3 - - - +
210T VAL* 1.3 56.5 + - - +
211T SER* 4.2 0.3 + - - -
219T CYS* 3.5 34.8 - - + +
233T CYS* 3.9 23.1 - - + -
234T GLU 2.9 10.1 + - - +
235T VAL* 3.3 9.6 - - + +
236T ILE* 2.7 32.4 + - - -
260T VAL* 3.4 7.4 - - + +
262T VAL* 3.9 14.8 - - + -
319T ILE* 4.6 6.5 - - + -
323T ILE* 3.7 27.8 - - + -
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Residues in contact with VAL 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208T THR* 3.8 8.5 - - + -
209T VAL* 1.3 74.3 - - - +
211T SER* 1.3 65.5 + - - +
236T ILE* 3.7 14.1 - - + +
238T MET* 3.6 27.5 - - + +
249T ILE* 3.7 45.8 - - + -
259T LEU* 3.8 12.8 - - + -
260T VAL 3.1 7.7 + - - +
261T THR* 3.2 10.8 - - + -
262T VAL* 2.8 24.9 + - - +
275T ILE* 3.9 7.6 - - + -
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Residues in contact with SER 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T VAL 4.2 0.2 + - - -
210T VAL* 1.3 77.7 - - - +
212T HIS* 1.3 71.3 + - - +
215T PRO* 3.9 5.0 - - - +
216T VAL* 3.6 21.3 + - - +
219T CYS* 3.6 24.2 - - - -
235T VAL* 6.3 0.9 - - - -
236T ILE 3.0 18.0 + - - +
238T MET* 3.2 21.9 + - - +
262T VAL* 2.6 27.1 + - - +
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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