Contacts of the strand formed by residues 311 - 317 (chain D) in PDB entry 4P0S
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 THR 311 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C VAL* 5.0 11.8 - - + +
292D THR* 3.9 10.7 - - - +
293D TRP* 3.9 28.0 - - + -
309D GLU* 2.5 17.1 + - - +
310D PRO* 1.3 87.7 + - - +
312D VAL* 1.3 65.2 + - - +
357D LYS* 3.2 19.5 + - - +
358D ALA* 3.5 19.6 - - + +
439D PHE* 4.1 20.6 - - + -
443D VAL* 4.8 6.2 - - + +
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Residues in contact with VAL 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 4.3 1.8 - - + -
290D SER* 4.1 9.6 - - - -
291D VAL 3.6 7.6 - - - +
292D THR* 3.7 20.6 - - + -
293D TRP* 4.4 0.4 - - - -
311D THR* 1.3 78.5 - - - +
313D LEU* 1.3 65.1 + - - +
314D VAL* 3.9 18.8 - - + -
350D ILE* 5.3 1.1 - - + -
354D THR* 3.7 26.0 - - + +
357D LYS* 3.4 31.4 - - + +
358D ALA 3.1 13.4 + - - +
359D LEU* 3.1 22.7 - - + +
360D SER* 3.5 0.9 + - - -
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Residues in contact with LEU 313 (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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290D SER* 3.6 0.5 - - - -
291D VAL* 2.7 54.5 + - + +
293D TRP* 4.1 11.6 - - + -
312D VAL* 1.3 74.5 - - - +
314D VAL* 1.3 72.8 + - - +
315D LEU* 4.3 4.0 - - + +
360D SER* 3.2 22.9 - - - +
362D VAL* 4.2 15.7 - - + -
432D LEU* 6.5 0.4 - - + -
435D PHE* 4.0 12.3 - - + -
436D THR* 5.9 4.7 - - + +
439D PHE* 3.4 45.3 - - + -
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Residues in contact with VAL 314 (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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287D VAL* 4.1 15.7 - - + -
288D PRO 4.8 1.3 - - - +
289D CYS 4.0 7.2 - - - +
290D SER* 3.6 19.3 - - - -
312D VAL* 3.9 8.5 - - + -
313D LEU* 1.3 78.4 - - - +
315D LEU* 1.4 66.6 + - - +
316D LEU* 5.4 0.2 - - + -
346D PHE* 4.8 7.6 - - + -
350D ILE* 4.1 21.5 - - + -
359D LEU* 3.3 23.4 - - + +
360D SER 3.0 16.0 + - - +
361D LEU* 2.8 43.0 - - + +
362D VAL 3.4 1.9 + - - -
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Residues in contact with LEU 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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260D LEU* 3.7 24.9 - - + -
263D MET* 3.5 28.0 - - + -
269D LEU* 5.3 0.9 - - + -
289D CYS* 3.1 35.2 + - + +
291D VAL* 5.8 0.4 - - - +
313D LEU* 4.3 4.9 + - + +
314D VAL* 1.4 76.0 - - - +
316D LEU* 1.3 82.1 + - - +
317D ARG 4.0 2.2 - - - +
362D VAL* 3.8 11.9 - - + +
364D VAL* 3.8 15.9 - - + -
429D TRP* 4.3 1.3 - - + -
432D LEU* 3.4 42.8 - - + -
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Residues in contact with LEU 316 (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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289D CYS* 6.0 2.5 - - - -
314D VAL 3.9 0.6 + - - -
315D LEU* 1.3 84.4 - - - +
317D ARG* 1.3 73.2 + - + +
320D ALA* 4.2 13.9 - - + -
321D PHE* 4.0 23.1 - - + +
324D MET* 3.7 27.6 - - + -
343D LEU* 6.2 0.4 - - + -
346D PHE* 4.3 24.5 - - + -
361D LEU* 3.9 32.1 - - + -
362D VAL 2.9 19.0 + - - +
363D ILE* 3.5 13.5 - - + +
364D VAL 3.7 3.5 + - - -
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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
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263D MET* 3.3 42.2 - - - +
264D GLU* 3.0 36.7 + - - -
289D CYS* 5.9 2.7 - - - -
315D LEU* 4.0 4.0 + - - +
316D LEU* 1.3 81.5 - - + +
318D ALA* 1.3 72.0 + - + +
319D GLU* 3.6 34.3 - - + +
320D ALA* 3.1 16.9 + - + +
321D PHE* 3.4 8.8 + - - +
363D ILE* 4.6 0.2 - - - -
364D VAL* 4.3 12.5 + - + +
429D TRP* 4.3 9.6 - - - -
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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