Contacts of the helix formed by residues 315 - 330 (chain D) in PDB entry 2I6A
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 PRO 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D ASP 3.7 1.5 - - - +
314D LYS* 1.3 96.1 - - + +
316D LEU* 1.3 57.2 + - - +
317D THR* 4.2 11.7 - - - +
318D GLU* 2.7 35.7 + - + +
319D CYS* 3.0 9.9 + - - -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ILE* 5.1 0.7 - - + -
261D ILE* 3.7 34.3 - - + -
273D MET* 3.2 31.9 - - + -
275D THR* 4.4 8.7 - - + -
306D PHE* 4.0 21.8 - - + -
310D LEU* 4.8 9.4 - - + -
314D LYS 3.5 2.3 + - - +
315D PRO* 1.3 72.5 - - - +
317D THR* 1.3 62.5 + - - +
319D CYS* 3.0 11.0 + - - +
320D ILE* 2.9 28.8 + - - +
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Residues in contact with THR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D PHE* 4.5 29.2 - - + -
315D PRO* 3.1 9.1 - - - +
316D LEU* 1.3 76.9 - - - +
318D GLU* 1.3 59.7 + - - +
320D ILE* 3.8 3.0 + - - +
321D ARG* 3.2 27.8 + - - +
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PHE* 3.0 34.0 - - + -
345A HIS 3.0 15.1 - - - +
309D GLN* 3.9 3.6 - - - +
314D LYS* 3.9 27.4 - - + -
315D PRO* 2.7 25.4 + - + +
317D THR* 1.3 82.5 - - - +
319D CYS* 1.3 60.7 + - - +
321D ARG* 2.3 39.4 + - - -
322D ALA 3.2 3.8 + - - -
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Residues in contact with CYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D PHE* 3.2 46.2 - - + +
309D GLN* 3.9 13.7 - - - -
310D LEU* 3.7 33.4 - - - -
314D LYS 3.8 12.6 - - - -
315D PRO 3.0 17.4 + - - -
316D LEU* 3.0 12.3 + - - +
318D GLU* 1.3 74.5 - - - +
320D ILE* 1.3 65.5 + - - +
322D ALA* 3.3 2.6 + - - +
323D GLY 3.1 16.5 + - - -
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Residues in contact with ILE 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D ILE* 4.1 9.6 - - + -
271D THR* 4.3 9.9 - - + -
273D MET* 3.4 31.6 - - + -
282D PHE* 3.7 38.4 - - + -
302D PHE* 3.6 10.5 - - + -
306D PHE* 3.9 13.0 - - + -
316D LEU 2.9 19.1 + - - +
317D THR* 3.9 5.6 - - - +
319D CYS* 1.3 74.5 - - - +
321D ARG* 1.3 59.1 + - - +
323D GLY* 2.9 3.3 + - - -
324D HIS* 2.8 53.3 + - + +
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Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PHE* 2.4 54.0 + - + -
345A HIS* 2.8 25.5 + - - +
285D LEU* 5.6 5.4 - - + +
317D THR* 3.2 13.5 + - - +
318D GLU* 2.3 54.6 + - - +
320D ILE* 1.3 81.8 - - - +
322D ALA* 1.3 55.0 + - - +
324D HIS* 3.4 10.9 + - + +
325D TYR* 3.0 23.4 + - - +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PHE* 2.8 39.5 - - + -
76D MET* 3.5 10.6 - - + +
305D GLY* 3.2 21.8 - - - +
309D GLN* 3.6 13.9 - - + -
318D GLU 3.2 2.6 + - - -
319D CYS 3.8 1.8 - - - +
321D ARG* 1.3 74.2 - - - +
323D GLY* 1.3 54.9 + - - +
325D TYR* 3.2 1.2 + - - +
326D ALA* 2.7 36.9 + - - +
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Residues in contact with GLY 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PHE* 3.1 50.0 - - - -
305D GLY* 4.0 1.1 - - - -
306D PHE 3.7 5.3 - - - +
319D CYS 3.1 7.6 + - - -
320D ILE 2.9 7.6 + - - -
322D ALA* 1.3 74.1 - - - +
324D HIS* 1.3 63.5 + - - +
327D ALA* 3.1 19.2 + - - +
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Residues in contact with HIS 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D THR* 2.7 30.4 + - - -
282D PHE* 3.9 11.0 + - + +
283D ALA 3.8 17.8 + - - -
284D VAL* 3.9 33.8 - - + +
285D LEU* 4.3 19.5 - - + +
287D GLN* 4.1 4.0 + - - -
302D PHE* 3.5 10.4 - + - -
320D ILE* 2.8 36.4 + - + +
321D ARG* 3.7 11.2 - - + +
323D GLY* 1.3 73.9 - - - +
325D TYR* 1.3 64.1 + - - +
327D ALA* 3.3 6.7 + - - +
328D SER* 3.1 22.9 + - - -
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Residues in contact with TYR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS* 5.6 4.9 - - - -
339A PRO* 5.2 2.1 - - - +
341A LYS 4.1 1.4 + - - -
342A PRO* 3.1 15.6 - - + +
343A ASP* 2.7 53.4 + - + +
344A PHE* 3.4 18.8 - - + -
75D TRP* 3.8 8.8 - + - -
76D MET* 3.3 26.9 - - + -
285D LEU* 4.0 17.2 - - + +
321D ARG 3.0 15.3 + - - +
322D ALA 3.2 6.5 + - - +
324D HIS* 1.3 77.4 - - - +
326D ALA* 1.3 61.4 + - - +
328D SER* 2.7 23.2 + - - -
329D ILE* 3.1 39.1 + - + +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 3.6 20.6 - - + -
75D TRP* 5.0 1.3 - - + -
76D MET* 4.7 7.6 - - + -
301D ALA* 3.3 25.0 - - - +
305D GLY* 3.9 6.1 - - - -
322D ALA 2.7 19.3 + - - +
323D GLY 4.1 0.2 - - - +
325D TYR* 1.3 79.8 - - - +
327D ALA* 1.3 57.3 + - - +
329D ILE* 4.8 3.4 - - - -
330D ILE* 2.9 38.7 + - + +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 6.3 1.3 - - + -
287D GLN* 4.2 8.8 - - - +
293D ILE* 6.1 1.0 - - - +
298D ALA* 3.7 36.3 - - + +
301D ALA* 4.0 10.9 - - - +
302D PHE* 4.3 4.9 - - + +
323D GLY 3.1 20.4 + - - +
324D HIS* 3.5 8.3 - - - +
325D TYR 3.2 0.2 - - - -
326D ALA* 1.3 78.7 - - - +
328D SER* 1.3 57.5 + - - +
329D ILE 3.7 0.2 + - - -
330D ILE 3.7 11.4 - - - +
331D ILE* 4.3 5.2 - - - +
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Residues in contact with SER 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS* 5.4 11.7 + - - +
285D LEU* 3.9 14.5 - - - +
287D GLN* 3.3 43.8 + - - +
324D HIS 3.1 7.5 + - - -
325D TYR* 2.7 20.0 + - - -
327D ALA* 1.3 74.8 - - - +
329D ILE* 1.3 68.8 + - - +
331D ILE* 2.7 22.8 - - - +
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS* 4.5 31.0 - - + +
337A THR 5.1 1.9 - - - +
338A PHE* 4.7 3.3 - - - -
339A PRO* 3.0 53.0 - - + +
75D TRP* 3.9 9.9 - - + -
325D TYR* 3.1 46.6 + - + +
326D ALA* 4.1 1.3 - - - +
328D SER* 1.3 82.9 + - - +
330D ILE* 1.3 66.4 + - + +
331D ILE* 2.7 31.9 + - - +
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Residues in contact with ILE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A PHE* 3.0 71.6 - - + -
72D VAL* 3.8 34.1 - - + -
75D TRP* 4.3 26.9 - - + -
297D GLY 4.6 7.6 - - - +
298D ALA* 5.3 0.3 - - - -
301D ALA* 4.2 11.1 - - + +
326D ALA 2.9 15.3 + - - +
327D ALA 3.7 11.8 - - - +
329D ILE* 1.3 85.2 - - + +
331D ILE* 1.3 58.2 + - - +
332D ARG 4.3 0.5 + - - -
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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