Contacts of the helix formed by residues 310 - 321 (chain D) in PDB entry 6IWQ
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 TRP 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D VAL* 4.7 3.8 - - + -
230D VAL* 4.4 11.4 - - + -
233D ARG 3.8 12.7 + - - -
234D THR* 3.1 27.4 + - + -
298D ILE* 3.6 33.4 - - + -
300D LEU* 4.3 9.6 - - + -
306D VAL* 3.1 40.8 - - + +
307D ALA 3.2 25.1 - - - +
308D VAL 3.1 3.1 - - - -
309D ASN* 1.3 79.4 - - - +
311D TYR* 1.3 78.5 + + + +
313D PRO* 3.1 3.6 - - - +
314D LEU* 3.3 37.8 - - + +
328D PRO* 6.0 0.7 - - + -
436D SER* 2.5 42.2 + - - +
437D ARG 3.9 16.8 - - - +
438D VAL* 4.4 7.9 - - + -
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Residues in contact with TYR 311 (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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135D PHE* 6.2 0.9 - + - -
206D LEU* 4.3 11.0 - - + -
207D LEU 2.5 27.4 + - - -
209D SER* 2.9 38.8 + - - -
211D VAL* 5.9 0.2 - - + -
233D ARG 5.1 0.7 - - - +
234D THR* 3.7 26.9 - - + -
235D PRO* 4.3 13.5 - - + -
238D TYR* 3.3 32.8 + + + -
298D ILE* 3.4 20.9 - - + -
309D ASN* 3.3 1.4 - - - +
310D TRP* 1.3 97.1 - + + +
312D ALA* 1.3 66.4 + - - +
314D LEU* 3.4 1.4 + - - -
315D VAL* 3.1 37.2 + - + +
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Residues in contact with ALA 312 (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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135D PHE* 3.8 16.8 - - + -
202D TYR* 3.3 30.1 - - + -
206D LEU* 3.8 22.9 - - + +
309D ASN* 3.6 12.8 + - - +
311D TYR* 1.3 76.3 - - - +
313D PRO* 1.3 66.5 - - + +
315D VAL 3.6 0.5 + - - -
316D ALA* 3.0 31.5 + - - +
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Residues in contact with PRO 313 (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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202D TYR* 3.3 31.2 - - + +
309D ASN* 3.0 28.3 - - - +
310D TRP 3.1 8.3 - - - +
312D ALA* 1.3 94.7 - - + +
314D LEU* 1.3 61.8 + - - +
316D ALA* 4.0 1.6 - - + +
317D PRO* 3.1 18.9 - - - +
381D PRO* 5.0 1.6 - - - +
433D VAL* 3.5 29.3 - - + +
435D CYS* 3.8 22.7 - - + +
436D SER* 4.2 0.2 - - - -
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Residues in contact with LEU 314 (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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298D ILE* 4.0 17.0 - - + -
310D TRP* 3.3 44.1 + - + +
311D TYR* 3.4 2.7 + - - +
312D ALA 3.3 0.4 - - - -
313D PRO* 1.3 82.3 - - - +
315D VAL* 1.3 59.6 + - + +
317D PRO* 3.4 3.8 - - - +
318D ILE* 4.4 2.3 - - - +
326D THR* 3.1 55.1 + - + +
327D VAL* 4.6 0.2 - - - -
328D PRO* 3.5 42.8 - - + -
392D PHE 5.7 0.4 - - - -
393D ALA* 4.0 20.6 - - + -
433D VAL* 4.3 0.7 - - - -
436D SER* 3.5 6.9 - - - +
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 4.4 4.9 - - + -
207D LEU* 3.9 30.7 - - + +
296D VAL* 4.2 17.7 - - + -
298D ILE* 4.2 11.9 - - + -
311D TYR* 3.1 47.4 + - + +
312D ALA 3.9 0.7 - - - +
314D LEU* 1.3 80.7 - - + +
316D ALA* 1.3 57.1 + - - +
317D PRO 3.3 1.6 - - - -
318D ILE* 3.5 12.0 + - + -
319D SER* 2.6 41.7 + - - +
393D ALA* 5.4 0.2 - - + -
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Residues in contact with ALA 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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122D TYR* 3.3 43.0 - - + +
124D ASP* 5.1 2.3 - - - +
125D PRO* 4.7 8.5 - - + -
202D TYR* 4.4 12.1 - - + -
206D LEU* 4.1 1.8 - - - -
312D ALA 3.0 19.9 + - - +
313D PRO* 4.0 5.4 - - + +
315D VAL* 1.3 78.2 - - - +
317D PRO* 1.3 69.7 - - + +
319D SER* 3.3 8.2 + - - -
320D LYS* 3.5 4.9 + - - +
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Residues in contact with PRO 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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124D ASP* 5.5 3.4 - - - +
313D PRO 3.1 18.8 - - - +
314D LEU 3.4 3.8 - - - +
316D ALA* 1.3 90.9 - - + +
318D ILE* 1.3 62.0 + - - +
319D SER 3.1 2.4 + - - -
320D LYS* 3.6 5.0 + - + +
321D ASP 3.3 9.5 + - - -
324D ILE* 3.3 40.0 - - + +
326D THR* 3.3 21.5 - - - +
381D PRO* 4.5 11.0 - - + -
431D LEU* 4.2 11.7 - - + -
433D VAL* 4.3 9.2 - - + -
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Residues in contact with ILE 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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118D GLN* 4.7 0.2 + - - -
207D LEU* 4.7 10.3 - - + +
296D VAL* 4.2 13.9 - - + -
314D LEU 4.4 6.3 - - - +
315D VAL* 3.5 12.7 + - + +
316D ALA 3.4 0.4 - - - -
317D PRO* 1.3 76.3 - - - +
319D SER* 1.3 63.1 + - - +
321D ASP 2.9 26.4 - - - +
322D ARG* 3.4 4.9 + - - +
324D ILE 3.6 19.3 - - - +
326D THR* 3.9 14.1 - - - +
393D ALA* 3.4 44.0 - - + +
394D ILE* 4.1 4.3 - - - +
395D GLU* 3.8 33.9 - - + +
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Residues in contact with SER 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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118D GLN* 2.9 26.2 + - - -
120D PHE* 4.0 7.4 - - - -
122D TYR* 3.5 32.5 + - - +
205D ASN 4.7 0.4 - - - -
206D LEU* 4.0 3.3 - - - -
207D LEU* 3.8 26.8 + - - +
315D VAL* 2.6 30.5 + - - +
316D ALA* 3.5 8.8 - - - -
317D PRO 3.1 1.0 - - - -
318D ILE* 1.3 75.5 - - - +
320D LYS* 1.4 60.4 + - - +
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Residues in contact with LYS 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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118D GLN* 3.5 16.2 + - - +
120D PHE 5.0 0.3 - - - +
121D THR* 6.0 0.2 - - - -
122D TYR* 3.4 34.2 + - + +
123D HIS* 3.9 15.1 + - - -
124D ASP* 3.6 57.0 + - - +
316D ALA 3.5 5.5 + - - +
317D PRO* 3.6 7.4 + - + +
318D ILE 3.5 0.2 - - - -
319D SER* 1.4 78.3 - - - +
321D ASP* 1.3 63.6 + - + +
324D ILE* 5.6 1.6 - - + -
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Residues in contact with ASP 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLN* 3.6 3.5 - - - +
317D PRO 3.3 7.7 + - - +
318D ILE* 2.9 13.4 + - - +
319D SER 3.1 1.4 - - - -
320D LYS* 1.3 82.8 - - + +
322D ARG* 1.3 60.1 + - - +
323D THR* 2.9 32.9 + - - +
324D ILE* 3.1 41.2 + - + +
429D LYS* 4.7 7.8 - - - +
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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
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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