Contacts of the strand formed by residues 336 - 345 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B ARG* 2.8 47.1 + - - +
277B CYS 3.8 10.0 - - - +
278B SER* 4.8 5.5 + - - -
334B ASP 3.4 5.3 + - - +
335B THR* 1.3 73.9 - - - +
337B VAL* 1.3 63.0 + - - +
338B SER* 4.4 9.2 + - - -
360B LYS 3.6 3.0 - - - +
362B GLY* 2.8 38.2 + - - +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 4.5 4.3 - - + -
275B PHE* 4.2 5.6 - - + -
276B ARG* 3.3 2.3 - - - +
277B CYS* 2.9 50.4 + - - -
279B CYS* 3.8 27.4 - - - -
285B MET* 4.4 12.3 - - + -
288B PHE* 3.6 37.0 - - + -
335B THR* 4.7 0.4 - - + -
336B ASP* 1.3 81.0 - - - +
338B SER* 1.3 63.6 + - - +
360B LYS 3.3 6.5 - - - +
361B VAL* 4.2 19.1 - - + -
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 3.2 23.2 - - - -
276B ARG* 3.9 16.3 + - - -
336B ASP* 4.2 9.7 + - - -
337B VAL* 1.3 76.3 - - - +
339B GLY* 1.3 57.5 + - - +
359B TYR* 3.4 4.3 - - - +
360B LYS* 2.7 50.8 + - - +
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 3.3 10.4 - - - +
275B PHE* 3.0 39.0 + - - +
338B SER* 1.3 78.7 - - - +
340B GLU* 1.3 60.3 + - - -
358B ARG* 3.1 15.0 - - - -
359B TYR* 4.0 1.1 - - - -
360B LYS* 5.7 0.2 - - - -
366B GLU* 5.9 3.6 - - - -
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLY* 3.6 13.9 - - - +
274B ARG* 3.1 48.9 + - + +
275B PHE* 4.0 2.2 - - - -
339B GLY* 1.3 75.2 - - - +
341B ILE* 1.3 67.6 + - - +
342B THR* 4.5 11.4 + - - +
356B LEU 3.7 1.0 - - - +
357B LEU* 3.5 5.5 - - - +
358B ARG* 2.7 56.4 + - + +
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ILE* 4.2 6.1 - - + -
253B PHE* 3.5 33.2 - - + -
272B GLY* 3.1 5.0 - - - -
273B GLY 3.0 36.2 + - - +
275B PHE* 4.3 10.8 - - + -
290B ILE* 3.6 31.9 - - + -
323B LEU* 3.9 7.9 - - + -
340B GLU* 1.3 76.4 - - - +
342B THR* 1.3 68.6 + - - +
343B LEU* 3.9 15.9 - - + -
355B VAL* 3.7 28.5 - - + -
356B LEU 3.4 3.6 - - - +
357B LEU* 4.2 7.4 - - + -
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ALA 4.8 2.9 - - - +
270B GLY* 3.8 27.6 - - - -
271B VAL 3.5 8.7 - - - +
272B GLY* 4.5 1.0 - - - +
340B GLU* 4.5 14.0 + - - +
341B ILE* 1.3 77.3 + - - +
343B LEU* 1.3 65.7 + - - +
344B LEU* 3.8 15.1 - - + +
354B ARG 3.7 0.7 - - - +
355B VAL* 3.3 4.9 - - - -
356B LEU* 2.9 46.1 + - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLY 3.2 26.5 - - - +
162B LEU* 4.2 17.3 - - + -
191B LEU* 3.8 27.4 - - + -
253B PHE* 4.2 9.0 - - + -
267B LEU 4.6 0.3 - - - +
270B GLY* 3.2 2.8 - - - -
271B VAL* 2.8 38.3 + - - +
290B ILE* 4.3 7.0 - - + -
341B ILE* 3.9 24.9 - - + -
342B THR* 1.3 77.3 - - - +
344B LEU* 1.3 66.0 + - - +
353B LEU* 4.0 16.2 - - + -
354B ARG 3.4 3.4 - - - -
355B VAL* 3.9 14.8 - - + -
403B GOL 4.5 3.3 - - - -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU 4.9 0.2 - - - -
268B GLU 4.3 4.9 - - - +
269B ALA 3.8 24.5 - - - +
270B GLY* 4.1 4.9 - - - -
342B THR* 3.8 25.4 - - + +
343B LEU* 1.3 78.1 - - - +
345B PRO* 1.3 79.6 - - + +
353B LEU* 3.8 1.0 - - - +
354B ARG* 2.7 69.7 + - + +
356B LEU* 4.7 11.4 - - + -
403B GOL 3.6 14.0 - - - -
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Residues in contact with PRO 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU 4.2 4.3 - - - +
268B GLU* 4.0 26.9 - - + +
344B LEU* 1.3 100.5 - - + +
346B SER* 1.3 65.3 + - - +
347B ARG 3.9 0.2 + - - -
350B PRO* 3.3 35.0 - - + +
352B ARG 3.7 5.4 - - - +
354B ARG* 4.0 11.8 + - - +
403B GOL 3.7 16.1 - - - +
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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