Contacts of the strand formed by residues 272 - 281 (chain A) in PDB entry 5DVX
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 LEU 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TYR* 4.1 2.0 - - - -
223A LEU* 4.9 3.1 - - + -
253A VAL* 5.3 7.0 - - + -
254A HIS 3.4 14.6 - - - +
255A LEU* 3.9 19.7 - - + -
262A VAL* 4.5 14.6 - - + -
265A ALA* 4.1 11.4 + - + +
266A LEU* 3.9 31.2 - - + -
267A GLY 5.6 0.9 - - - +
268A ARG 4.7 0.8 + - - -
270A GLY 4.1 5.4 - - - -
271A GLY* 1.3 82.6 - - - +
273A ALA* 1.3 63.1 + - - +
274A VAL* 5.9 0.4 - - + -
331A LEU* 4.0 22.9 - - + -
337A ALA* 5.9 0.4 - - + -
339A GLY 4.7 1.2 + - - -
340A VAL* 3.5 21.3 - - + -
341A ILE* 3.0 21.7 + - - +
403A GOL 4.6 7.6 - - - -
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Residues in contact with ALA 273 (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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212A MET* 4.3 11.2 - - + -
214A LEU* 4.4 3.6 - - + -
220A TYR* 3.5 38.3 - - + +
254A HIS* 2.7 41.8 + - + +
272A LEU* 1.3 75.0 - - - +
274A VAL* 1.3 64.9 + - - +
275A LEU 4.3 0.2 - - - -
340A VAL* 4.4 0.2 - - - -
341A ILE* 3.3 16.4 - - + +
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Residues in contact with VAL 274 (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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251A HIS* 3.8 16.8 - - + +
252A VAL 3.4 10.3 - - - +
253A VAL* 4.3 19.7 - - + -
272A LEU* 5.9 0.7 - - + -
273A ALA* 1.3 79.9 - - - +
275A LEU* 1.3 76.5 + - - +
331A LEU* 5.2 5.8 - - + -
340A VAL* 3.9 19.7 - - + -
341A ILE 2.9 8.3 + - - +
342A TRP* 3.4 42.7 - - + -
343A THR* 3.0 28.1 + - - +
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Residues in contact with LEU 275 (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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180A LEU* 4.0 20.0 - - + -
182A LEU* 4.6 8.7 - - + -
185A PHE* 5.4 1.3 - - + -
212A MET* 4.0 31.0 - - + -
214A LEU* 4.5 0.9 - - + -
250A ILE 3.6 0.9 - - - +
251A HIS* 3.4 4.7 - - - -
252A VAL* 2.8 43.7 + - + +
254A HIS* 3.8 21.3 - - + +
273A ALA 4.3 0.2 - - - -
274A VAL* 1.3 74.2 - - - +
276A ALA* 1.3 60.7 + - - +
317A LEU* 4.3 23.5 - - + +
343A THR* 3.6 27.4 - - + +
345A PHE* 4.5 16.4 - - + -
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Residues in contact with ALA 276 (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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249A GLU* 3.7 13.0 - - - +
250A ILE 3.2 4.0 - - - -
251A HIS* 3.7 21.3 - - + -
275A LEU* 1.3 74.7 - - - +
277A ALA* 1.3 60.2 + - - +
317A LEU* 5.7 0.4 - - - -
342A TRP* 4.1 12.6 - - + -
343A THR 2.9 13.2 + - - +
344A VAL* 3.4 17.2 - - + +
345A PHE* 3.0 31.5 + - - -
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Residues in contact with ALA 277 (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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249A GLU* 3.3 7.6 - - - +
250A ILE* 2.9 47.8 + - + +
276A ALA* 1.3 75.4 - - - +
278A PHE* 1.3 67.6 + - - +
279A LEU* 5.2 0.2 - - + -
317A LEU* 4.6 1.8 - - + +
318A PRO* 3.6 35.9 - - + -
344A VAL* 5.4 0.7 - - - -
345A PHE* 4.0 9.2 - - + +
347A GLN 4.8 0.4 - - - +
349A VAL* 4.8 3.4 - - + -
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Residues in contact with PHE 278 (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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166A ILE* 4.8 1.1 - - + -
237A SER* 3.9 7.4 - - - -
239A HIS* 3.4 41.7 - - + -
241A VAL* 3.7 30.7 - - + -
246A PHE* 3.6 41.5 - + + -
248A ALA 3.6 2.5 - - - -
249A GLU* 3.5 21.5 - - - -
277A ALA* 1.3 74.6 - - - +
279A LEU* 1.3 59.8 + - - +
325A PHE* 6.5 0.2 - + - -
344A VAL* 3.9 20.2 - - + -
345A PHE 4.6 10.7 + - - -
346A ASN 5.7 1.3 - - - -
347A GLN 5.1 0.8 + - - -
348A THR* 3.5 18.9 - - + +
349A VAL* 3.0 27.5 + - - +
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Residues in contact with LEU 279 (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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227A LEU* 4.4 10.3 - - + -
246A PHE* 4.3 0.9 - - - +
247A PRO* 3.2 22.3 - - - +
248A ALA* 2.9 45.2 + - + +
249A GLU* 3.9 0.9 - - - +
250A ILE* 3.8 12.1 - - + +
277A ALA 3.7 11.7 - - - +
278A PHE* 1.3 76.0 - - - +
280A GLU* 1.3 61.3 + - - +
289A TYR* 3.6 34.1 - - + +
349A VAL* 3.3 26.5 - - + +
351A LEU* 3.9 24.5 - - + -
356A LEU* 4.6 4.7 - - + -
359A LEU* 4.5 5.8 - - + -
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Residues in contact with GLU 280 (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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246A PHE* 3.6 32.8 - - + -
247A PRO* 4.0 7.4 - - + -
279A LEU* 1.3 74.9 - - - +
281A GLU* 1.3 66.7 + - - +
348A THR* 2.7 37.4 + - - +
349A VAL 2.8 10.6 + - - +
350A SER* 3.2 8.9 + - - +
351A LEU* 2.8 27.2 + - - +
356A LEU* 4.1 5.6 - - - -
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Residues in contact with GLU 281 (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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247A PRO* 4.2 6.5 - - + +
280A GLU* 1.3 78.8 - - - +
282A GLY* 1.3 72.8 + - - +
350A SER* 4.4 3.1 + - - -
351A LEU 3.3 4.3 - - - -
353A ALA* 3.5 36.4 - - - +
356A LEU* 3.8 14.8 - - + +
194B ARG* 4.4 18.9 + - - +
305B GLU* 4.8 7.3 - - - +
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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