Contacts of the helix formed by residues 310 - 321 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C VAL* 4.5 8.1 - - + -
230C VAL* 4.2 11.7 - - + -
233C ARG 3.5 14.7 + - - -
234C THR* 2.9 30.7 + - + -
298C ILE* 3.6 41.1 - - + -
300C LEU* 4.5 9.9 - - + -
306C VAL* 3.3 36.2 - - + +
307C ALA 3.3 19.7 - - - +
308C VAL 3.2 2.7 + - - -
309C ASN* 1.3 77.6 - - - +
311C TYR* 1.3 80.8 + + + +
313C PRO* 3.3 2.4 - - - +
314C LEU* 3.2 28.3 - - + +
328C PRO* 6.4 0.2 - - + -
435C CYS 4.7 0.2 - - - -
436C SER* 2.4 41.2 + - - +
437C ARG 4.0 16.4 - - - +
438C VAL* 4.6 5.8 - - + -
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Residues in contact with TYR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 6.4 0.2 - + - -
206C LEU* 4.2 7.6 - - + -
207C LEU 2.6 26.2 + - - -
209C SER* 3.4 19.1 + - - -
211C VAL* 6.1 0.4 - - + -
233C ARG 5.2 0.4 - - - +
234C THR* 3.9 22.0 - - + -
235C PRO* 4.4 11.2 - - + -
238C TYR* 3.4 43.4 + + + +
239C LEU* 6.3 0.4 - - + -
298C ILE* 3.5 24.5 - - + -
309C ASN* 3.3 1.6 - - - +
310C TRP* 1.3 101.2 - + + +
312C ALA* 1.3 66.2 + - + +
314C LEU* 3.3 1.6 + - - +
315C VAL* 2.9 62.9 + - + +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.6 41.1 - - + -
202C TYR* 3.7 13.7 - - + -
206C LEU* 4.4 8.3 - - + +
235C PRO* 6.3 0.2 - - - +
309C ASN* 3.7 10.7 + - - +
311C TYR* 1.3 81.4 - - + +
313C PRO* 1.3 67.5 - - + +
316C ALA* 3.0 33.7 + - - +
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Residues in contact with PRO 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TYR* 3.4 31.9 - - + +
309C ASN* 3.2 30.7 - - - +
310C TRP 3.3 8.7 - - - +
312C ALA* 1.3 96.1 - - + +
314C LEU* 1.3 55.2 + - - +
316C ALA* 4.7 0.4 - - + -
317C PRO* 3.1 22.7 - - - +
381C PRO* 5.0 1.4 - - - +
433C VAL* 3.5 30.0 - - + +
435C CYS* 3.8 20.2 - - + +
436C SER* 4.2 0.2 - - - -
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ILE* 4.0 17.5 - - + -
310C TRP* 3.2 43.7 + - + +
311C TYR 3.3 2.8 + - - +
313C PRO* 1.3 80.5 - - - +
315C VAL* 1.3 62.9 + - + +
317C PRO* 3.4 3.3 - - - +
318C ILE* 4.3 2.4 - - - +
326C THR* 3.2 53.9 + - + +
327C VAL* 4.6 0.2 - - - -
328C PRO* 3.5 41.5 - - + -
392C PHE 5.7 0.7 - - - -
393C ALA* 4.0 20.6 - - + -
433C VAL* 4.3 0.7 - - - -
436C SER* 3.5 7.7 - - - +
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Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 4.1 5.2 - - + -
207C LEU* 3.7 26.7 - - + +
209C SER* 4.4 0.9 - - - +
296C VAL* 4.1 21.3 - - + -
298C ILE* 4.2 11.9 - - + -
311C TYR* 2.9 50.6 + - + +
312C ALA 4.6 0.4 - - - +
314C LEU* 1.3 83.2 - - + +
316C ALA* 1.3 59.7 + - - +
317C PRO 3.4 0.4 - - - -
318C ILE* 3.3 9.4 + - + +
319C SER* 2.7 36.8 + - - +
393C ALA* 5.5 1.1 - - + -
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 3.0 37.0 - - + +
124C ASP* 5.6 0.7 - - - -
125C PRO* 4.7 6.5 - - + -
202C TYR* 4.3 12.1 - - + -
206C LEU* 4.8 4.0 - - + +
312C ALA 3.0 19.8 + - - +
313C PRO 4.4 1.1 - - - +
315C VAL* 1.3 76.5 - - - +
317C PRO* 1.3 69.6 - - + +
319C SER* 3.0 21.2 + - - -
320C LYS* 3.3 6.4 + - - +
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Residues in contact with PRO 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ASP* 5.4 3.8 - - - +
313C PRO 3.1 26.2 - - - +
314C LEU 3.4 5.2 - - - +
316C ALA* 1.3 85.4 - - + +
318C ILE* 1.3 59.3 + - - +
319C SER 3.3 0.2 + - - -
320C LYS* 3.6 5.0 + - + +
321C ASP 3.3 9.5 + - - -
324C ILE* 3.3 39.7 - - + +
326C THR* 3.3 20.6 - - - +
381C PRO* 4.5 11.7 - - + -
431C LEU* 4.2 11.7 - - + -
433C VAL* 4.3 9.2 - - + -
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLN* 4.5 0.2 + - - -
207C LEU* 4.5 5.0 - - + +
296C VAL* 4.3 16.8 - - + -
314C LEU 4.3 5.6 - - - +
315C VAL* 3.3 10.7 + - + +
316C ALA 3.3 0.6 - - - -
317C PRO* 1.3 77.2 - - - +
319C SER* 1.3 62.7 + - - +
321C ASP 2.9 26.4 - - - +
322C ARG* 3.4 4.9 + - - -
324C ILE 3.6 17.9 - - - +
326C THR* 3.9 14.8 - - - +
393C ALA* 3.4 44.2 - - + +
394C ILE* 4.1 5.6 - - - +
395C GLU* 3.8 33.9 - - + +
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 3.2 17.2 - - - +
120C PHE* 3.8 7.6 - - - +
122C TYR* 3.5 32.7 - - - +
206C LEU* 3.8 4.6 - - - -
207C LEU* 2.2 43.2 + - - +
315C VAL 2.7 18.6 + - - -
316C ALA* 3.0 10.6 + - - -
318C ILE* 1.3 75.6 - - - +
320C LYS* 1.4 64.4 + - - +
321C ASP 3.3 0.2 + - - -
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Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 3.2 18.6 + - - +
120C PHE 4.8 1.0 - - - +
122C TYR* 3.5 39.2 + - + +
123C HIS* 4.4 5.8 - - - +
124C ASP* 3.0 56.0 + - - +
316C ALA 3.3 5.6 + - - +
317C PRO* 4.2 6.7 - - + +
318C ILE 3.5 0.2 - - - -
319C SER* 1.4 76.6 - - - +
321C ASP* 1.3 61.7 + - + +
324C ILE* 5.6 1.6 - - + -
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Residues in contact with ASP 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 3.3 3.4 + - - +
317C PRO 3.3 7.7 + - - +
318C ILE* 2.9 12.9 + - - +
319C SER 3.1 1.0 - - - -
320C LYS* 1.3 83.4 - - + +
322C ARG* 1.3 60.9 + - - +
323C THR* 2.9 33.0 + - - +
324C ILE* 3.1 40.7 + - + +
429C LYS* 4.7 8.0 - - - +
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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
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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