Contacts of the strand formed by residues 314 - 319 (chain D) in PDB entry 2IHU
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 LYS 314 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LEU* 4.1 31.6 - - + +
215D GLU* 5.5 3.4 + - - -
289D ASP 3.0 13.0 + - - +
290D LEU* 3.3 19.8 - - + -
291D VAL 2.9 24.4 + - - -
313D LYS* 1.3 77.7 - - - +
315D THR* 1.3 63.1 + - - +
332D ASP* 3.3 28.9 - - + +
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Residues in contact with THR 315 (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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212D LEU* 4.8 0.2 - - - +
290D LEU* 4.7 0.4 - - - -
291D VAL* 3.3 12.1 - - + -
307D TRP* 3.5 38.4 - - + +
313D LYS* 4.8 6.3 - - + +
314D LYS* 1.3 80.1 - - - +
316D VAL* 1.3 64.6 + - - +
317D ARG 4.2 0.4 - - - -
329D TYR* 3.7 16.6 - - + -
330D ARG 4.3 2.3 + - - -
331D PRO* 3.4 19.3 - - - +
332D ASP* 2.9 35.8 + - - +
333D VAL 3.1 6.9 + - - -
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ALA* 3.6 34.5 - - + +
212D LEU* 4.2 11.9 - - + -
290D LEU* 4.0 19.7 - - + -
291D VAL 2.9 6.3 + - - +
292D LEU* 3.5 18.0 - - + -
293D THR* 2.8 31.0 + - - +
315D THR* 1.3 75.9 - - - +
317D ARG* 1.3 61.7 + - - +
318D ILE* 3.8 18.9 - - + +
329D TYR* 3.8 2.7 - - - -
333D VAL* 3.2 12.8 - - + +
335D VAL* 4.0 13.2 - - + -
342D PHE* 5.3 0.2 - - + -
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Residues in contact with ARG 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D THR* 3.4 7.9 - - - +
296D TYR* 4.4 19.2 + - + +
316D VAL* 1.3 72.6 - - - +
318D ILE* 1.3 62.3 + - - +
319D SER* 3.5 15.4 + - - +
321D THR* 3.0 44.0 + - - -
322D VAL 3.6 1.2 + - - -
323D ASN* 3.4 39.1 + - - +
324D PRO* 3.8 6.7 - - - +
329D TYR* 3.7 27.7 + - + +
331D PRO* 3.7 17.2 - - + +
333D VAL 2.9 7.7 + - - +
334D ASP* 2.8 38.9 + - - +
335D VAL* 2.7 33.4 + - - +
336D VAL* 4.0 4.4 - - - +
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Residues in contact with ILE 318 (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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292D LEU* 4.4 5.8 - - + -
293D THR 3.0 17.8 + - - +
294D VAL* 4.1 14.6 - - + -
295D GLY* 2.7 34.5 + - - +
296D TYR 3.2 5.2 + - - -
316D VAL* 3.8 20.9 - - + +
317D ARG* 1.3 76.1 - - - +
319D SER* 1.3 63.0 + - - +
335D VAL* 3.3 15.7 - - + +
337D THR* 4.6 5.2 - - + +
339D VAL* 4.5 17.3 - - + -
342D PHE* 3.7 64.4 - - + -
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Residues in contact with SER 319 (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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226D ALA* 5.8 0.2 - - - +
295D GLY* 4.7 0.6 - - - -
296D TYR 3.6 18.2 + - - -
317D ARG* 3.5 29.2 + - - +
318D ILE* 1.3 78.6 - - - +
320D PRO* 1.3 70.6 - - - +
321D THR* 2.8 29.9 + - - +
335D VAL 3.1 6.3 + - - -
336D VAL* 3.3 8.0 - - - -
337D THR 3.0 21.9 + - - -
339D VAL* 4.9 0.2 - - - -
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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