Contacts of the helix formed by residues 304 - 319 (chain X) in PDB entry 5A31
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 304 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271X VAL* 2.9 39.5 - - + +
294X PHE* 6.3 1.1 - - + -
297X ALA* 3.1 46.7 - - + +
298X GLN* 3.9 2.5 - - - +
301X ASP* 3.6 16.6 - - + +
303X TYR* 1.3 81.8 - - - +
305X ILE* 1.3 68.0 + - - +
306X LYS* 3.3 4.7 + - + +
307X GLY* 3.5 9.1 + - - +
308X MET* 3.1 42.8 + - + +
331X LEU* 5.4 0.6 - - - +
334X ILE* 4.9 1.4 - - - +
54Y ARG* 5.6 5.2 - - - +
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Residues in contact with ILE 305 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X TYR 3.9 1.5 - - - -
304X LEU* 1.3 74.6 - - - +
306X LYS* 1.3 61.6 - - - +
308X MET* 3.4 5.9 + - - +
331X LEU* 4.3 9.9 - - + -
334X ILE* 3.8 23.1 - - + -
335X SER* 3.2 25.1 - - - +
338X HIS* 3.7 36.8 - - + +
340X GLU* 3.1 54.6 - - + +
341X PRO* 4.5 1.1 - - + -
92Y GLU* 4.0 27.1 + - + +
95Y ASN* 5.0 3.8 - - - +
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Residues in contact with LYS 306 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X LEU* 5.8 4.4 - - - +
272X ASP* 3.9 25.5 + - - +
275X GLY* 6.5 1.1 - - - -
304X LEU* 3.3 3.5 - - + -
305X ILE* 1.3 78.9 - - - +
307X GLY* 1.3 64.0 + - - +
308X MET 3.4 0.3 + - - -
309X ASP* 3.8 14.2 - - - +
310X VAL* 4.6 5.4 + - - +
340X GLU* 4.4 10.6 - - - +
54Y ARG* 5.6 13.9 - - - +
55Y LEU* 5.0 13.4 - - - +
92Y GLU* 6.2 0.4 - - - +
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Residues in contact with GLY 307 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275X GLY* 5.3 13.4 - - - -
279X ASP* 6.1 0.2 - - - -
294X PHE* 3.3 22.7 - - - -
297X ALA* 6.6 0.2 - - - -
304X LEU* 3.5 12.2 + - - +
305X ILE 3.4 0.4 - - - -
306X LYS* 1.3 80.1 - - - +
308X MET* 1.3 64.0 + - - +
310X VAL* 3.1 19.7 + - - +
311X TYR 3.2 7.8 + - - -
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Residues in contact with MET 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294X PHE* 3.2 29.4 - - + -
298X GLN* 3.8 36.8 - - + +
301X ASP 5.4 0.2 - - - +
302X PRO 5.2 3.4 - - - +
304X LEU* 3.1 43.1 - - + +
305X ILE 3.4 4.7 + - - +
306X LYS 3.3 1.2 - - - -
307X GLY* 1.3 72.9 - - - +
309X ASP* 1.3 58.6 + - - +
311X TYR* 4.1 1.1 - - - -
312X GLY* 2.7 33.4 + - - -
327X LEU* 3.9 24.3 - - + +
331X LEU* 3.6 34.3 - - + -
340X GLU* 4.9 0.9 - - + -
344X VAL* 5.2 2.6 - - - +
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Residues in contact with ASP 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305X ILE 4.0 3.0 + - - -
306X LYS 3.8 10.5 + - - +
308X MET* 1.3 78.7 - - - +
310X VAL* 1.3 68.7 + - + +
312X GLY* 3.6 5.4 + - - -
313X TYR 3.9 5.9 + - - -
340X GLU* 3.5 33.0 - - + +
343X VAL* 3.1 24.8 - - - +
344X VAL* 5.7 1.8 + - - +
347X CYS* 4.6 1.9 - - - -
372X SER* 4.1 17.5 - - - -
374X GLN* 3.0 41.2 - - - +
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Residues in contact with VAL 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278X ALA* 4.9 5.4 - - + +
279X ASP* 2.9 32.5 - - - +
282X PHE* 3.9 35.2 - - + -
294X PHE* 5.6 1.6 - - + -
306X LYS 4.7 4.7 - - - +
307X GLY* 3.1 9.7 + - - +
309X ASP* 1.3 88.3 - - + +
311X TYR* 1.3 65.7 + - - +
313X TYR* 3.2 20.3 + - - +
314X LEU* 3.5 10.5 + - + +
374X GLN* 4.4 17.5 - - - +
406X ARG* 6.4 0.2 - - - +
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Residues in contact with TYR 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291X VAL* 4.1 21.4 - - + +
294X PHE* 2.8 67.3 - + + -
295X GLU* 4.2 17.7 + - + +
298X GLN* 4.3 14.6 + - - -
307X GLY 3.2 0.6 + - - -
308X MET* 3.1 3.1 + - - +
310X VAL* 1.3 78.6 - - - +
312X GLY* 1.3 64.2 + - - +
314X LEU* 3.4 21.2 + - + +
315X LEU* 3.3 50.6 + - + +
320X ARG* 5.0 2.8 + - - -
323X ASP* 5.5 1.2 + - - +
327X LEU* 3.4 25.8 - - + -
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Residues in contact with GLY 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308X MET 2.7 19.5 + - - -
309X ASP 3.6 2.9 + - - -
310X VAL 3.4 0.2 - - - -
311X TYR* 1.3 74.4 - - - +
313X TYR* 1.3 60.9 + - - +
315X LEU* 3.2 17.1 + - - +
316X ALA* 3.3 10.4 + - - +
324X VAL* 3.9 7.4 - - - +
327X LEU* 4.3 13.2 - - - -
344X VAL* 4.5 11.9 - - - -
347X CYS* 3.8 12.1 - - - +
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Residues in contact with TYR 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282X PHE* 3.1 35.9 - + + -
309X ASP 3.9 1.2 + - - -
310X VAL 3.2 12.3 + - - +
312X GLY* 1.3 75.8 - - - +
314X LEU* 1.3 62.0 + - - +
316X ALA* 3.2 14.3 + - - +
317X ARG* 3.2 19.9 + - + -
347X CYS* 3.5 20.8 - - - -
350X PHE* 4.9 13.0 - + - -
351X TYR* 4.1 21.9 + + - -
374X GLN* 3.7 27.1 - - - +
377X LEU* 4.4 18.2 - - + -
378X LEU* 5.6 0.4 - - + -
408X ASP* 4.1 15.0 + - - -
411X GLU* 5.3 2.3 + - - -
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Residues in contact with LEU 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X ALA* 5.6 2.0 - - + +
282X PHE* 3.2 35.9 - - + -
287X ASN* 3.5 37.4 - - - +
290X SER* 3.7 20.9 - - - +
291X VAL* 3.5 28.8 - - + +
294X PHE* 5.4 3.4 - - + -
310X VAL* 3.5 7.5 + - + +
311X TYR* 3.4 26.4 + - + +
312X GLY 3.3 0.6 - - - -
313X TYR* 1.3 76.0 - - - +
315X LEU* 1.3 63.3 + - + +
317X ARG* 3.4 6.2 + - - +
318X GLU* 2.9 27.7 + - - +
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Residues in contact with LEU 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291X VAL* 4.9 5.8 - - + -
311X TYR* 3.3 54.1 - - + +
312X GLY* 3.2 2.5 + - - +
314X LEU* 1.3 79.4 - - + +
316X ALA* 1.3 52.6 + - - +
318X GLU* 3.1 7.4 + - + -
319X GLY 2.8 30.0 + - - -
320X ARG* 3.0 43.4 + - + +
323X ASP* 3.5 35.2 - - + +
324X VAL* 3.5 20.6 - - + +
327X LEU* 4.5 4.9 - - + -
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Residues in contact with ALA 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312X GLY 3.3 9.1 + - - +
313X TYR* 3.2 12.9 + - + +
315X LEU* 1.3 78.1 - - - +
317X ARG* 1.3 60.1 - - - +
319X GLY* 3.1 14.0 + - - +
320X ARG 5.1 0.4 - - - +
321X LEU* 5.7 4.3 - - + -
324X VAL* 4.4 5.5 - - + +
347X CYS* 4.4 8.1 - - + +
351X TYR* 3.1 60.5 - - + -
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Residues in contact with ARG 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282X PHE* 6.1 0.9 - - + -
287X ASN* 4.2 19.5 - - - +
313X TYR* 3.2 21.1 + - + +
314X LEU* 3.8 8.5 - - - +
316X ALA* 1.3 77.8 - - - +
318X GLU* 1.3 60.0 + - - +
319X GLY* 3.5 0.9 + - - -
351X TYR* 4.1 7.4 + - - +
509X CYS* 5.2 10.0 - - - +
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Residues in contact with GLU 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ASN* 5.4 5.5 - - - +
291X VAL* 6.4 1.6 - - + -
314X LEU 2.9 14.1 + - - +
315X LEU* 3.1 14.1 + - + +
317X ARG* 1.3 75.4 - - - +
319X GLY* 1.3 59.6 + - - +
320X ARG* 3.4 23.9 + - + +
538X LEU 5.6 1.4 - - - +
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Residues in contact with GLY 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315X LEU 2.8 9.8 + - - -
316X ALA* 3.1 15.6 + - - -
317X ARG 3.3 1.0 - - - -
318X GLU* 1.3 74.0 - - - +
320X ARG* 1.3 57.0 + - - -
321X LEU* 3.1 15.0 + - - +
351X TYR* 5.8 1.3 - - - -
538X LEU 6.0 2.0 - - - -
539X ASP* 6.4 2.0 - - - -
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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
------------------------------------------------------------
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