Contacts of the helix formed by residues 297 - 312 (chain A) in PDB entry 5D0B
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 LYS 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ILE* 4.3 20.0 - - + +
279A SER 5.2 0.4 - - - +
280A ASN* 3.0 23.2 + - - +
283A PHE* 3.6 35.7 - - + -
296A GLY* 1.3 73.9 - - - -
298A LYS* 1.3 62.4 + - - +
299A PRO 3.4 0.7 - - - -
300A ILE* 3.1 5.5 + - + +
301A GLN* 2.8 63.0 + - + +
329A ARG* 3.8 7.0 - - - +
505A GOL 2.9 35.3 + - - +
30F G 3.0 29.7 + - - -
31F A 5.5 0.6 + - - -
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Residues in contact with LYS 298 (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 LYS* 3.6 41.5 + - - +
295A ARG 5.6 0.7 - - - +
296A GLY* 3.4 0.4 - - - -
297A LYS* 1.3 80.6 - - - +
299A PRO* 1.3 68.5 - - + +
301A GLN* 3.2 3.6 + - - +
302A ARG* 2.9 23.4 + - - +
329A ARG* 3.8 35.4 - - + +
331A VAL* 4.9 14.6 - - + +
332A ILE* 4.1 12.2 - - + +
505A GOL 4.8 4.0 - - - +
31F A 3.1 30.7 + - - +
32F C 4.3 15.6 + - - -
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Residues in contact with PRO 299 (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 THR 3.6 18.4 - - - +
220A GLN* 4.3 6.1 - - - +
221A THR 4.0 15.3 - - - +
222A LYS* 4.2 20.2 - - + -
295A ARG* 4.0 27.6 - - + +
296A GLY 3.9 12.1 - - - +
297A LYS 3.7 1.6 - - - -
298A LYS* 1.3 93.9 - - + +
300A ILE* 1.3 61.3 + - + +
302A ARG* 3.5 6.0 + - + +
303A ASN* 3.0 34.7 + - - +
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Residues in contact with ILE 300 (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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96A PHE* 3.8 29.6 - - + -
237A LEU* 3.9 27.1 - - + +
238A TYR* 5.3 1.3 - - + -
275A LEU* 4.5 24.0 - - + -
283A PHE* 3.9 30.1 - - + -
287A PHE* 5.6 0.4 - - + -
292A GLY 3.4 27.4 - - - +
293A SER* 4.5 0.9 - - - -
296A GLY 4.0 7.0 - - - +
297A LYS* 3.1 8.2 + - - +
299A PRO* 1.3 80.5 - - + +
301A GLN* 1.3 60.3 + - + +
303A ASN* 3.3 3.3 + - - +
304A ALA* 2.9 26.0 + - - +
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Residues in contact with GLN 301 (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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275A LEU* 2.9 31.2 + - + +
276A LEU* 3.6 22.1 + - + +
278A ILE* 3.6 16.3 + - + +
297A LYS* 2.8 35.9 + - + +
298A LYS 3.8 3.6 - - - +
300A ILE* 1.3 76.4 - - + +
302A ARG* 1.3 65.7 + - - +
304A ALA* 3.1 8.4 + - - +
305A ILE* 2.9 29.8 + - + +
329A ARG* 2.8 40.5 + - - +
332A ILE* 4.3 8.5 - - + -
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Residues in contact with ARG 302 (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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218A LEU 2.8 25.4 + - - -
219A THR* 3.7 8.5 + - - +
221A THR* 2.9 31.9 + - - -
222A LYS 5.7 0.4 - - - -
223A GLY 2.7 37.3 + - - -
224A PHE* 4.8 0.2 - - - +
225A LEU* 3.8 25.8 - - - +
298A LYS 2.9 17.4 + - - +
299A PRO* 3.7 5.1 + - + +
301A GLN* 1.3 75.3 - - - +
303A ASN* 1.3 81.3 + - - +
305A ILE* 3.3 12.3 + - - +
306A LEU* 3.1 37.8 + - + +
331A VAL* 3.9 16.8 - - + -
332A ILE* 4.2 4.8 - - + +
335A THR* 3.9 23.8 - - + +
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Residues in contact with ASN 303 (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 THR* 3.0 36.3 + - - +
225A LEU* 5.1 1.7 - - - +
233A ILE* 5.3 5.4 - - + +
236A ARG 3.6 18.1 - - - +
237A LEU* 2.9 29.8 + - - +
299A PRO 3.0 12.9 + - - +
300A ILE 3.7 4.5 - - - +
302A ARG* 1.3 98.7 + - - +
304A ALA* 1.3 60.6 + - - +
306A LEU* 3.4 12.8 + - - +
307A ALA* 2.8 29.6 + - - +
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Residues in contact with ALA 304 (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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237A LEU* 3.6 15.9 - - + +
272A LEU* 4.0 18.1 - - + +
275A LEU* 4.2 13.7 - - + -
276A LEU* 4.2 11.9 - - + -
300A ILE 2.9 14.7 + - - +
301A GLN* 3.1 13.2 + - - +
303A ASN* 1.3 75.6 - - - +
305A ILE* 1.3 65.2 + - - +
307A ALA* 3.3 2.9 + - - +
308A LEU* 3.1 29.4 + - - +
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Residues in contact with ILE 305 (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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276A LEU* 3.6 16.2 - - + -
301A GLN* 2.9 21.0 + - + +
302A ARG* 3.4 11.4 - - - +
304A ALA* 1.3 76.1 - - - +
306A LEU* 1.3 62.4 + - - +
308A LEU* 3.0 21.3 + - - +
309A ALA* 3.0 11.8 + - - +
320A LEU* 3.8 14.1 - - + -
323A LEU* 4.4 9.0 - - + -
332A ILE* 4.0 37.2 - - + +
335A THR* 3.6 24.0 - - + +
336A ALA* 4.3 4.0 - - + +
339A ALA* 3.6 24.8 - - + +
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Residues in contact with LEU 306 (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* 3.6 37.2 - - + -
230A ARG* 4.3 27.1 - - + +
233A ILE* 5.2 9.2 - - + -
234A GLY 4.5 1.5 - - - +
302A ARG* 3.1 25.0 + - + +
303A ASN* 3.7 17.3 - - - +
304A ALA 3.4 0.2 - - - -
305A ILE* 1.3 79.9 - - - +
307A ALA* 1.3 56.9 + - - +
309A ALA* 3.3 7.5 + - - +
310A HIS* 3.0 26.2 + - - +
335A THR* 3.7 19.7 - - + -
338A TRP* 3.7 27.7 - - + -
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Residues in contact with ALA 307 (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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234A GLY 3.5 20.4 - - - +
235A ASN* 3.8 15.9 - - + -
236A ARG 5.5 0.2 - - - +
237A LEU* 4.9 0.9 - - + -
272A LEU* 3.6 22.0 - - + -
303A ASN 2.8 18.4 + - - +
304A ALA 3.5 7.2 - - - +
305A ILE 3.2 0.2 - - - -
306A LEU* 1.3 76.5 - - - +
308A LEU* 1.3 57.9 + - - +
310A HIS* 3.2 3.5 - - - +
311A PHE* 3.0 35.1 + - - -
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Residues in contact with LEU 308 (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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92A ARG* 4.3 4.9 - - + -
272A LEU* 3.8 31.6 - - + -
273A LYS* 4.4 7.4 - - + -
276A LEU* 3.7 30.7 - - + -
304A ALA 3.1 19.5 + - - +
305A ILE* 3.0 9.7 + - - +
307A ALA* 1.3 74.3 - - - +
309A ALA* 1.3 59.2 + - - +
311A PHE* 3.2 3.3 + - - +
312A LYS 2.8 23.0 + - - -
313A ASP* 3.1 42.5 + - + +
316A ALA* 3.8 20.2 - - + -
320A LEU* 4.9 8.7 - - + -
343A ILE* 4.3 3.2 - - + +
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Residues in contact with ALA 309 (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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305A ILE 3.0 6.9 + - - +
306A LEU 3.5 9.2 - - - +
308A LEU* 1.3 77.4 - - - +
310A HIS* 1.3 61.5 + - - +
312A LYS* 3.1 22.7 + - - +
338A TRP* 3.9 21.1 - - + -
339A ALA* 3.8 28.9 - - + +
342A LYS* 4.0 17.6 - - + +
343A ILE* 4.2 11.1 - - - +
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Residues in contact with HIS 310 (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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230A ARG 5.7 4.6 + - - +
231A THR* 5.1 11.4 + - - -
234A GLY* 3.7 40.1 + - - +
235A ASN 4.6 0.2 - - - -
306A LEU 3.0 13.5 + - - +
307A ALA 3.2 9.2 - - - +
309A ALA* 1.3 78.6 - - - +
311A PHE* 1.3 85.0 + + - +
312A LYS* 3.6 3.6 + - - +
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Residues in contact with PHE 311 (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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87A SER* 4.6 4.5 - - - -
92A ARG* 3.3 73.2 + - + +
93A ARG 3.9 10.3 - - - -
235A ASN* 3.6 40.2 - - + -
272A LEU* 4.1 6.7 - - + -
307A ALA 3.0 27.3 + - - +
308A LEU* 3.2 6.0 + - - +
309A ALA 3.2 0.2 - - - -
310A HIS* 1.3 90.4 - + - +
312A LYS* 1.3 70.3 + - - +
313A ASP* 3.3 3.5 + - - +
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Residues in contact with LYS 312 (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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308A LEU 2.8 9.1 + - - -
309A ALA 3.1 14.6 + - - +
310A HIS 4.9 3.0 + - - +
311A PHE* 1.3 80.4 - - - +
313A ASP* 1.3 57.6 + - - +
314A ALA* 3.1 9.2 + - - +
342A LYS* 3.2 42.9 + - - +
343A ILE* 3.8 28.9 - - - +
344A GLY* 5.8 0.4 - - - -
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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