Contacts of the strand formed by residues 336 - 345 (chain A) in PDB entry 4Y2H
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 ASP 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A CYS 3.5 7.0 - - - +
278A SER* 3.1 21.0 + - - -
334A ASP 3.1 6.4 + - - +
335A THR* 1.3 71.5 - - - +
337A VAL* 1.3 60.8 + - - +
338A SER* 4.3 1.6 - - - -
360A LYS 3.9 1.1 - - - +
361A VAL* 3.9 0.2 - - - -
362A GLY* 2.7 40.2 + - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PRO* 4.5 3.1 - - + -
275A PHE* 4.3 4.8 - - + -
276A ARG* 3.3 2.1 - - - +
277A CYS* 2.8 47.5 + - - +
279A CYS* 3.8 27.1 - - - -
285A MET* 4.2 13.0 - - + -
288A PHE* 3.6 37.9 - - + -
335A THR* 4.2 0.9 - - + +
336A ASP* 1.3 79.0 - - - +
338A SER* 1.3 63.7 + - - +
360A LYS 3.5 7.0 - - - +
361A VAL* 4.2 20.4 - - + -
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.5 21.3 - - - -
276A ARG* 4.0 10.5 - - - -
336A ASP* 5.7 1.8 - - - -
337A VAL* 1.3 76.0 - - - +
339A GLY* 1.3 57.6 + - - +
359A TYR* 3.2 4.5 - - - +
360A LYS* 2.7 56.9 + - - +
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Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.2 14.8 - - - +
275A PHE* 2.9 36.9 + - - +
338A SER* 1.3 79.2 - - - +
340A GLU* 1.3 60.1 + - - -
358A ARG* 3.0 15.3 - - - -
359A TYR* 4.0 0.9 - - - -
360A LYS* 5.8 0.2 - - - -
366A GLU* 6.1 0.7 - - - -
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLY* 3.5 13.2 - - - +
274A ARG* 2.8 38.1 + - + +
275A PHE* 3.5 3.5 - - - -
339A GLY* 1.3 75.3 - - - +
341A ILE* 1.3 61.6 + - - +
342A THR* 5.0 7.6 + - - +
356A LEU 3.8 1.2 - - - +
357A LEU* 3.5 4.2 - - - +
358A ARG* 2.8 68.5 + - + +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 4.0 10.5 - - + -
253A PHE* 3.7 31.6 - - + -
272A GLY* 3.4 3.0 - - - -
273A GLY* 3.0 34.9 + - - +
275A PHE* 4.2 16.8 - - + -
290A ILE* 3.8 29.2 - - + -
323A LEU* 4.0 5.6 - - + -
340A GLU* 1.3 74.9 - - - +
342A THR* 1.3 68.8 + - - +
343A LEU* 3.9 18.6 - - + -
355A VAL* 3.9 22.9 - - + -
356A LEU 3.4 4.3 - - - +
357A LEU* 4.4 5.2 - - + -
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA 4.5 4.9 - - - +
270A GLY* 4.0 25.8 - - - -
271A VAL 3.5 5.2 - - - +
272A GLY* 5.4 1.0 - - - -
273A GLY 5.2 0.9 + - - -
340A GLU* 5.0 7.6 + - - +
341A ILE* 1.3 78.2 + - - +
343A LEU* 1.3 68.0 + - - +
344A LEU* 4.0 13.2 + - + +
354A ARG 3.7 0.5 - - - +
355A VAL* 3.3 6.2 - - - +
356A LEU* 2.9 48.9 + - + +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY 3.2 26.9 - - - +
162A LEU* 4.2 17.3 - - + +
191A LEU* 3.6 29.2 - - + -
253A PHE* 3.9 13.2 - - + -
267A LEU 4.9 0.9 - - - +
270A GLY* 3.4 1.6 - - - -
271A VAL* 2.7 40.5 + - + +
290A ILE* 4.2 6.7 - - + -
341A ILE* 3.9 21.8 - - + -
342A THR* 1.3 76.3 - - - +
344A LEU* 1.3 63.4 + - - +
353A LEU* 4.1 11.9 - - + -
354A ARG 3.6 2.9 - - - -
355A VAL* 3.9 24.2 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 6.1 0.4 - - - -
267A LEU 5.1 0.2 - - - -
268A GLU 4.6 8.1 - - - +
269A ALA 4.5 13.2 - - - +
270A GLY* 4.2 8.5 - - - +
342A THR* 4.4 7.9 - - + +
343A LEU* 1.3 77.2 - - - +
345A PRO* 1.3 78.0 - - + +
353A LEU* 3.6 7.3 - - - +
354A ARG* 2.6 75.7 + - + +
356A LEU* 3.8 35.4 - - + -
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Residues in contact with PRO 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 4.1 7.2 - - - +
267A LEU 4.1 14.8 - - - +
268A GLU* 4.8 8.7 - - - +
344A LEU* 1.3 103.3 - - + +
346A SER* 1.3 64.6 + - - +
347A ARG* 3.8 0.7 + - - -
350A PRO* 3.2 31.9 - - + +
352A ARG 3.7 7.2 - - - +
353A LEU* 4.9 0.9 - - - -
354A ARG* 4.3 3.8 + - - +
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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