Contacts of the strand formed by residues 248 - 256 (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 ALA 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LEU* 6.0 0.2 - - + -
228A HIS 3.2 16.6 - - - +
229A TRP* 4.1 10.8 - - + -
237A SER* 3.7 12.5 - - - +
246A PHE* 3.3 1.1 + - - +
247A PRO* 1.3 81.7 - - - +
249A GLU* 1.3 64.9 + - - +
278A PHE* 3.6 4.5 - - - +
279A LEU* 2.9 46.4 + - + +
356A LEU* 4.5 6.5 - - + -
359A LEU* 4.1 9.2 - - + -
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Residues in contact with GLU 249 (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* 3.4 6.1 - - - +
228A HIS* 2.9 38.5 + - + +
237A SER* 3.6 9.1 - - - -
238A GLU* 2.8 23.7 + - - +
239A HIS* 2.8 33.7 + - - -
248A ALA* 1.3 78.9 - - - +
250A ILE* 1.3 63.8 + - - +
251A HIS* 2.7 33.7 + - + +
276A ALA* 3.7 5.7 - - - +
277A ALA 3.3 17.7 - - - +
278A PHE* 3.5 16.7 - - + -
279A LEU* 3.9 4.7 - - - +
344A VAL* 6.2 0.7 - - - -
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Residues in contact with ILE 250 (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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225A LEU* 4.2 22.0 - - + -
226A HIS 3.6 6.5 - - - +
227A LEU* 3.6 20.6 - - + -
249A GLU* 1.3 73.8 - - - +
251A HIS* 1.3 74.5 + - - +
252A VAL* 4.5 7.6 - - + -
275A LEU 3.6 0.6 - - - +
276A ALA* 3.2 7.3 - - - -
277A ALA* 2.9 57.3 + - + +
279A LEU* 3.8 4.2 - - + +
289A TYR* 3.4 27.4 - - + +
316A LEU* 4.0 21.8 - - + +
317A LEU* 4.2 11.9 - - + -
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Residues in contact with HIS 251 (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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225A LEU* 3.1 5.7 - - - +
226A HIS* 3.0 48.6 + - + +
228A HIS* 3.1 9.6 + + - -
238A GLU* 3.1 23.3 - - + -
239A HIS* 5.3 0.2 - + - -
249A GLU* 2.7 32.5 + - + +
250A ILE* 1.3 86.0 - - - +
252A VAL* 1.3 61.8 + - - +
253A VAL* 4.0 1.4 + - + -
274A VAL* 3.8 12.8 - - + -
275A LEU 3.4 2.7 - - - -
276A ALA* 3.7 11.0 - - + -
332A THR* 4.7 0.2 - - + -
342A TRP* 3.6 22.7 - + - -
401A ZN 2.0 33.7 - - - -
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Residues in contact with VAL 252 (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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185A PHE* 4.7 9.6 - - + -
206A LEU* 4.1 18.8 - - + -
222A ALA* 4.2 4.5 - - + -
224A GLN 3.6 9.2 - - - +
225A LEU* 4.0 17.9 - - + -
250A ILE* 4.5 5.2 - - + -
251A HIS* 1.3 75.5 - - - +
253A VAL* 1.3 60.0 + - - +
254A HIS* 3.0 32.2 + - + +
274A VAL* 3.4 1.9 - - - -
275A LEU* 2.8 39.9 + - + +
313A ILE* 5.2 3.1 - - + -
317A LEU* 4.1 32.1 - - + -
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Residues in contact with VAL 253 (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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222A ALA* 3.7 2.4 - - - +
223A LEU* 2.8 37.4 + - + +
224A GLN* 2.9 36.6 + - + +
226A HIS* 3.8 21.3 - - + -
252A VAL* 1.3 74.3 - - - +
254A HIS* 1.3 62.2 + - - +
272A LEU* 5.3 6.5 - - + -
273A ALA 3.7 5.2 - - - +
274A VAL* 4.3 21.1 - - + -
331A LEU* 5.4 6.7 - - + -
403A GOL 3.9 27.8 - - - +
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Residues in contact with HIS 254 (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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185A PHE* 3.9 8.0 - + - -
212A MET* 3.5 38.9 - - + +
220A TYR* 3.6 17.5 - - + -
221A ARG 3.2 7.9 - - - +
222A ALA* 3.5 29.9 - - + +
223A LEU* 4.4 5.2 - - - +
252A VAL* 3.0 44.7 + - + -
253A VAL* 1.3 74.5 - - - +
255A LEU* 1.3 59.6 + - - +
272A LEU* 3.4 12.0 - - - +
273A ALA 2.7 40.5 + - - +
275A LEU* 3.8 22.8 + - + -
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Residues in contact with LEU 255 (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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220A TYR* 3.4 3.1 - - - -
221A ARG* 2.9 43.6 + - + +
223A LEU* 4.0 28.9 - - + +
254A HIS* 1.3 73.2 - - - +
256A SER* 1.3 80.3 + - - +
259A TYR* 3.5 19.1 - - + +
260A ALA 3.8 15.0 - - - +
261A ARG* 3.9 18.4 - - - +
262A VAL* 4.1 4.7 - - + +
265A ALA* 3.5 33.2 - - + -
271A GLY 3.7 1.8 - - - +
272A LEU* 3.9 7.2 - - + -
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Residues in contact with SER 256 (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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219A GLU 3.6 3.9 + - - -
220A TYR* 3.3 16.8 - - - -
255A LEU* 1.3 76.2 - - - +
257A THR* 1.3 59.2 + - - +
258A LYS* 2.9 36.7 + - - +
259A TYR* 3.0 32.4 + - - +
270A GLY 3.6 16.7 + - - -
271A GLY* 2.8 23.0 + - - -
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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