Contacts of the strand formed by residues 207 - 211 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D HIS* 1.3 82.9 - - + +
208D THR* 1.3 72.7 + - - +
209D VAL* 4.4 4.0 - - + -
231D VAL* 4.9 0.9 - - + -
232D GLU 3.5 2.6 + - - +
233D CYS* 3.4 27.2 - - + +
234D GLU 3.0 23.6 + - - -
256D THR* 3.5 12.4 - - - +
258D HIS* 3.7 12.8 - - + +
260D VAL* 3.8 25.8 - - + -
323D ILE* 4.0 25.1 - - + -
326D THR* 3.8 23.3 - - + -
327D LEU* 4.2 10.8 - - + -
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Residues in contact with THR 208 (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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207D ILE* 1.3 73.4 - - - +
209D VAL* 1.3 62.9 + - - +
210D VAL* 3.9 13.0 - - + -
234D GLU 3.6 4.9 - - - +
236D ILE* 3.6 24.9 - - + -
249D ILE 4.7 4.7 - - - +
252D SER* 2.6 34.9 + - - +
253D VAL* 3.6 7.3 + - - -
256D THR* 2.7 20.5 + - - +
258D HIS 3.0 14.7 + - - -
259D LEU* 3.4 5.1 - - + +
260D VAL 2.9 26.3 + - - +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D ILE* 4.4 6.3 - - + -
208D THR* 1.3 75.5 - - - +
210D VAL* 1.3 60.7 + - - +
211D SER* 4.8 0.3 - - - -
219D CYS* 3.6 32.1 - - + +
233D CYS* 3.8 21.1 - - + -
234D GLU 2.9 11.6 + - - +
235D VAL* 3.4 11.7 - - + +
236D ILE 2.9 24.6 + - - +
260D VAL* 3.3 11.2 - - + +
262D VAL* 4.4 10.8 - - + -
319D ILE* 4.8 1.6 - - + -
323D ILE* 3.6 32.8 - - + -
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Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D THR* 4.1 7.6 - - + -
209D VAL* 1.3 70.9 - - - +
211D SER* 1.3 66.6 + - - +
236D ILE* 3.7 13.0 - - + +
238D MET* 3.9 26.3 - - + +
249D ILE* 3.7 43.3 - - + -
259D LEU* 3.4 26.2 - - + -
260D VAL 3.1 3.8 + - - -
261D THR* 3.2 13.7 - - + -
262D VAL* 2.9 25.1 + - - +
275D ILE* 4.3 5.6 - - + -
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Residues in contact with SER 211 (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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209D VAL 4.8 0.7 - - - -
210D VAL* 1.3 79.6 - - - +
212D HIS* 1.3 66.9 + - - +
215D PRO* 4.0 2.8 - - - +
216D VAL* 3.6 24.7 + - - -
219D CYS* 3.7 23.3 - - - -
235D VAL* 5.8 0.7 - - - -
236D ILE 3.0 11.3 + - - +
237D ASN* 3.5 2.8 - - - -
238D MET* 3.0 32.1 + - - +
262D VAL* 2.7 24.7 + - - +
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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