Contacts of the helix formed by residues 312 - 328 (chain A) in PDB entry 5W97
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 ILE 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 4.0 20.0 - - + +
280A ILE* 4.2 15.7 - - + +
283A LEU* 3.4 48.5 - - + +
284A GLY* 3.9 7.6 - - - +
287A VAL* 4.6 6.5 - - + -
308A ALA 4.3 3.6 - - - +
309A THR* 3.4 22.9 - - + +
310A MET 3.1 0.8 - - - -
311A ILE* 1.3 76.7 - - - +
313A ALA* 1.3 60.2 + - - +
314A ILE 3.2 0.7 + - - -
315A PRO* 3.3 4.9 - - - +
316A THR* 2.7 34.4 + - - +
602A HEA 3.4 29.6 - - + +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR 4.5 0.6 + - - -
310A MET 3.2 15.3 + - - +
311A ILE 3.0 0.2 + - - -
312A ILE* 1.3 78.4 - - - +
314A ILE* 1.3 57.8 + - - +
316A THR* 3.8 3.4 - - - -
317A GLY* 2.8 26.2 + - - -
356A ILE* 4.0 12.5 - - + +
602A HEA 3.8 44.3 - - + +
69B PRO* 5.2 1.5 - - + +
73B LEU* 4.1 14.8 - - + -
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 4.5 4.9 - - + -
311A ILE* 3.0 19.5 + - + +
313A ALA* 1.3 73.8 - - - +
315A PRO* 1.3 76.0 - - + +
317A GLY* 3.2 10.0 + - - -
318A VAL* 3.2 14.1 + - + +
65B TRP 4.9 2.0 - - - +
66B THR* 4.3 27.8 - - + +
69B PRO* 4.5 9.6 - - + +
70B ALA* 3.8 35.7 - - + +
73B LEU* 3.9 20.2 - - + -
303c PEK 4.4 33.2 - - + -
30g LEU* 6.2 0.7 - - + -
103g CDL 5.9 1.8 - - + -
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Residues in contact with PRO 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 3.9 18.6 - - + -
276A ALA* 3.4 43.4 - - - +
279A SER* 3.9 19.1 - - - -
280A ILE* 3.9 12.6 - - + -
283A LEU* 4.2 11.7 - - + -
311A ILE 3.2 12.6 - - - +
312A ILE 3.3 12.3 - - - +
314A ILE* 1.3 94.0 - - + +
316A THR* 1.3 60.5 + - - +
318A VAL* 3.2 9.4 + - + +
319A LYS* 3.5 2.1 + - - +
303c PEK 4.8 4.9 - - + -
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 4.2 12.6 - - + -
280A ILE* 3.8 14.2 - - + +
312A ILE* 2.7 34.0 + - - +
313A ALA 4.0 2.7 - - - -
314A ILE 3.2 1.0 - - - -
315A PRO* 1.3 77.8 - - - +
317A GLY* 1.3 63.7 + - - +
319A LYS* 3.1 15.2 + - + +
320A VAL* 3.1 13.4 + - + +
323A TRP* 6.5 0.2 - - + -
348A PHE* 3.7 34.1 - - + -
602A HEA 3.7 24.5 + - + +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA 2.8 13.4 + - - -
314A ILE* 3.6 2.2 - - - -
316A THR* 1.3 76.7 - - - +
318A VAL* 1.3 61.0 + - - +
320A VAL* 3.0 3.4 + - - +
321A PHE* 3.0 35.4 + - - -
602A HEA 3.5 34.0 - - - +
65B TRP 5.0 2.7 - - - -
69B PRO* 5.8 0.9 - - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLY 3.9 21.8 - - - +
273A MET* 4.1 7.0 - - + -
275A TRP* 3.9 18.4 - - + -
276A ALA* 4.4 1.6 - - + -
314A ILE 3.2 14.5 + - - +
315A PRO 3.4 9.4 - - - +
316A THR 3.2 0.6 - - - -
317A GLY* 1.3 74.3 - - - +
319A LYS* 1.3 54.4 + - - +
321A PHE* 3.4 1.7 + - - +
322A SER* 2.8 37.7 + - - +
62B GLU* 3.8 21.1 - - - +
65B TRP* 4.1 24.6 + - + +
66B THR* 3.7 23.1 - - - +
303B CHD 5.0 0.2 - - + -
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 5.3 0.4 - - - +
251A PHE* 3.6 49.1 - - + -
255A SER* 4.7 5.1 + - - -
273A MET* 3.3 51.3 + - + +
276A ALA* 3.6 20.2 - - + -
277A MET* 3.7 20.5 - - + +
280A ILE* 4.5 4.0 - - + -
315A PRO 3.5 4.7 + - - +
316A THR* 3.1 9.7 + - + +
318A VAL* 1.3 73.0 - - - +
320A VAL* 1.3 67.2 + - - +
322A SER* 3.1 3.1 + - - -
323A TRP* 3.0 48.0 + - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 3.1 12.7 + - + +
317A GLY 3.0 8.2 + - - +
319A LYS* 1.3 76.8 - - - +
321A PHE* 1.3 65.5 + - + +
323A TRP* 3.3 24.4 + - + +
324A LEU* 3.3 29.1 + - + +
345A ILE* 4.2 16.6 - - + +
348A PHE* 4.7 9.6 - - + -
349A THR* 3.8 20.4 - - - +
602A HEA 3.9 28.0 - - + -
38B VAL* 4.6 13.0 - - + -
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY* 3.0 28.3 + - - +
318A VAL 4.0 0.2 - - - +
320A VAL* 1.3 76.3 - - + +
322A SER* 1.3 56.8 + - - +
324A LEU* 3.3 19.9 + - + +
325A ALA* 2.9 27.7 + - - +
602A HEA 4.3 32.8 - - + -
34B ILE* 5.8 2.2 - - + -
37B LEU* 5.4 3.6 - - + -
38B VAL* 4.3 20.2 - - + -
41B ILE* 5.0 6.7 - - + -
65B TRP* 3.4 52.9 - + + -
69B PRO* 4.9 1.6 - - + -
302B PSC 3.7 49.2 - - + +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 3.7 18.4 + - - +
269A GLY 4.9 0.2 + - - -
273A MET* 3.2 32.6 - - - +
318A VAL* 2.8 24.3 + - - +
319A LYS 3.1 0.8 + - - -
321A PHE* 1.3 74.8 - - - +
323A TRP* 1.3 56.2 + - - +
325A ALA* 3.4 8.6 + - - +
326A THR* 2.6 37.6 + - - -
62B GLU* 4.1 6.8 + - - -
65B TRP* 3.8 11.4 - - - -
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Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.5 51.6 - + - -
254A ILE* 3.8 14.6 - - + -
255A SER* 2.9 35.9 + - - +
258A VAL* 3.7 8.9 - - + +
267A PRO* 6.3 2.2 - - + -
273A MET* 4.7 6.0 - - - -
319A LYS* 3.0 38.8 + - + -
320A VAL* 3.6 32.3 - - + +
322A SER* 1.3 74.5 - - - +
324A LEU* 1.3 61.5 + - - +
326A THR* 3.3 9.4 + - + -
327A LEU* 3.1 31.2 + - - +
344A PHE* 3.8 20.0 - + - -
345A ILE* 3.8 34.1 - - + -
348A PHE* 5.3 1.6 - + - -
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Residues in contact with LEU 324 (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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320A VAL* 3.3 21.9 + - + +
321A PHE* 3.6 31.2 - - + +
322A SER 3.3 0.2 - - - -
323A TRP* 1.3 76.9 - - - +
325A ALA* 1.3 63.8 + - - +
327A LEU* 3.2 19.5 + - + +
328A HIS 3.1 17.3 + - - -
345A ILE* 4.1 14.8 - - + -
38B VAL* 4.7 11.9 - - + +
41B ILE* 3.9 30.3 - - + -
42B ILE* 3.4 34.3 - - + +
45B MET* 3.5 10.1 - - + +
302B PSC 4.4 6.3 - - + -
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Residues in contact with ALA 325 (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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264A LYS* 4.0 3.5 + - - -
268A PHE* 3.4 37.2 - - + +
321A PHE 2.9 18.1 + - - +
322A SER 3.7 0.9 - - - +
323A TRP 3.3 0.2 - - - -
324A LEU* 1.3 77.9 - - - +
326A THR* 1.3 58.8 + - - +
328A HIS* 3.2 23.0 - - - +
56B MET* 4.1 9.5 - - - +
65B TRP* 3.8 4.3 - - + -
302B PSC 3.8 24.0 - - + +
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Residues in contact with THR 326 (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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255A SER 5.4 0.2 - - - +
258A VAL* 3.9 12.8 - - + +
259A THR* 3.8 36.1 - - - +
262A SER* 3.9 1.8 - - - -
264A LYS* 2.9 39.0 + - + +
266A GLU 4.6 0.2 - - - +
267A PRO* 3.8 12.0 - - + +
268A PHE* 3.0 21.8 + - - +
322A SER 2.6 22.4 + - - -
323A TRP* 3.4 9.4 - - - -
324A LEU 3.1 0.2 - - - -
325A ALA* 1.3 74.2 - - - +
327A LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 327 (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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258A VAL* 4.0 9.6 - - + -
262A SER* 3.7 8.5 - - - +
323A TRP 3.1 20.2 + - - +
324A LEU* 3.4 28.3 - - + +
326A THR* 1.3 76.8 - - - +
328A HIS* 1.3 55.3 + - - +
329A GLY 3.1 1.0 + - - -
330A GLY* 2.9 25.1 + - - -
332A ILE* 3.7 9.5 - - + +
338A MET* 3.3 34.3 - - + -
342A LEU* 3.9 22.2 - - + -
345A ILE* 4.7 5.2 - - + -
42B ILE* 5.3 2.7 - - + -
45B MET* 4.0 23.6 - - + +
46B LEU* 4.2 15.3 - - + -
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS* 2.9 24.6 + - - -
324A LEU 3.1 7.6 + - - +
325A ALA* 3.2 17.0 - - - +
326A THR 3.2 0.4 - - - -
327A LEU* 1.3 72.3 - - - +
329A GLY* 1.3 60.2 + - - +
45B MET* 3.6 29.4 - - - +
52B HIS* 5.8 1.2 - - - -
56B MET* 3.4 29.9 - - + +
302B PSC 3.9 27.1 - - + +
13I LEU* 3.7 33.8 + - + +
14I ALA* 5.4 2.2 + - - -
17I LEU* 3.7 36.8 - - + +
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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
------------------------------------------------------------
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