Contacts of the helix formed by residues 306 - 317 (chain C) in PDB entry 4IG9
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 306 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302C PHE* 3.2 49.3 - - + +
303C ARG 4.7 3.6 - - - +
304C LYS 4.1 4.5 - - - +
305C ASP* 1.3 86.8 - - - +
307C ARG* 1.3 64.4 + - + +
308C PRO* 3.6 0.9 - - - -
309C PHE 3.6 3.1 + - - -
310C PHE* 3.1 32.1 + - + -
392C VAL* 4.0 24.0 - - + -
406C ILE* 5.0 5.4 - - + -
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Residues in contact with ARG 307 (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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287C PHE* 3.9 31.8 - - + -
305C ASP* 3.0 28.7 + - - +
306C PRO* 1.3 78.6 - - + +
308C PRO* 1.4 68.7 - - + +
310C PHE* 3.1 16.0 + - - +
311C LYS* 3.2 13.5 + - - +
390C GLN 5.8 3.6 - - - +
392C VAL* 4.3 18.2 - - + -
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Residues in contact with PRO 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.7 11.8 - - + +
287C PHE* 3.9 29.6 - - + -
290C LEU* 3.9 24.0 - - + -
296C MET* 4.9 6.9 - - + +
301C TYR* 3.9 19.5 - - + +
305C ASP* 3.3 32.8 - - - +
307C ARG* 1.4 91.4 - - + +
309C PHE* 1.3 61.6 + - + +
311C LYS* 3.7 1.3 + - - +
312C PHE* 3.3 21.3 + - - +
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Residues in contact with PHE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C MET* 3.1 30.3 - - + +
297C PHE* 4.5 6.3 - + - -
302C PHE* 3.8 31.2 - + + -
306C PRO 3.9 1.6 - - - +
307C ARG 3.2 0.8 - - - -
308C PRO* 1.3 81.5 - - + +
310C PHE* 1.3 71.9 + + - +
311C LYS 3.3 0.2 - - - -
312C PHE* 3.3 28.5 + + - +
313C ALA* 2.8 26.7 + - + +
366C PHE* 4.2 20.9 - + - -
409C PRO* 4.0 27.8 - - + -
411C ILE* 4.2 13.0 - - + -
413C PHE* 3.5 28.7 - + - -
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Residues in contact with PHE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PHE* 3.7 5.6 - + - -
306C PRO* 3.1 21.7 + - + -
307C ARG* 3.1 8.7 + - - +
309C PHE* 1.3 93.7 - + - +
311C LYS* 1.3 62.4 + - - +
313C ALA* 3.7 3.8 - - + -
314C LYS* 3.6 2.9 + - - +
387C ILE* 3.3 49.5 - - + +
390C GLN* 5.2 10.6 - - - +
391C VAL 5.7 0.2 - - - +
392C VAL* 3.6 33.4 - - + -
393C PRO* 3.6 31.9 - - + -
406C ILE* 3.5 27.1 - - + -
407C MET 4.0 1.6 - - - -
409C PRO* 3.8 20.0 - - + -
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Residues in contact with LYS 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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279C ILE* 5.3 0.4 - - - -
282C ARG* 4.6 10.1 + - - +
283C LEU* 3.7 24.2 - - + +
286C ASP* 3.5 21.8 + - - -
287C PHE* 4.0 17.3 - - + -
307C ARG 3.2 13.8 + - - +
308C PRO 4.1 4.7 - - - +
310C PHE* 1.3 75.6 - - - +
312C PHE* 1.3 63.8 + - - +
313C ALA 3.2 0.2 - - - -
314C LYS* 3.4 24.1 - - - +
315C GLU* 4.0 21.2 + - - +
390C GLN* 3.8 36.8 - - + +
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Residues in contact with PHE 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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273C PHE* 3.6 21.3 - + + -
279C ILE* 3.6 35.0 - - + -
283C LEU* 4.3 3.7 - - + +
296C MET* 4.1 14.6 - - - -
297C PHE* 3.4 35.2 - + - -
308C PRO 3.3 17.0 + - - +
309C PHE* 3.3 30.7 + + - +
311C LYS* 1.3 80.2 - - - +
313C ALA* 1.3 62.6 + - - +
315C GLU* 3.5 14.2 + - - +
316C ILE* 3.4 37.8 + - + +
347C ILE* 4.6 4.3 - - + -
366C PHE* 4.4 13.0 - + - -
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Residues in contact with ALA 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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309C PHE* 2.8 23.4 + - + +
310C PHE* 3.9 7.6 - - + +
311C LYS 3.2 0.6 - - - -
312C PHE* 1.3 76.5 - - - +
314C LYS* 1.3 56.2 + - - +
315C GLU 3.1 4.9 + - - -
316C ILE* 3.5 1.8 + - - +
317C TYR* 3.1 31.7 + - - +
366C PHE* 3.7 30.4 - - + -
387C ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 314 (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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310C PHE 3.6 3.4 + - - +
311C LYS* 3.4 21.1 - - - +
312C PHE 3.4 0.2 - - - -
313C ALA* 1.3 77.9 - - - +
315C GLU* 1.3 62.5 + - + +
317C TYR* 4.2 8.4 - - - +
320C GLN* 2.8 26.3 + - - +
387C ILE* 3.5 37.7 - - + +
388C PHE* 3.8 26.0 + - + +
390C GLN* 2.8 39.5 + - + +
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Residues in contact with GLU 315 (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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271C PRO* 4.2 17.0 - - + +
279C ILE* 3.3 29.3 - - + +
282C ARG* 3.7 21.8 + - - +
311C LYS* 4.0 24.0 + - - +
312C PHE 3.7 7.9 - - - +
313C ALA 3.1 1.0 - - - -
314C LYS* 1.3 85.2 - - + +
316C ILE* 1.3 65.5 + - + +
317C TYR 3.3 0.4 - - - -
320C GLN* 2.8 15.8 - - - +
321C PHE* 3.1 20.8 - - + -
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Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 4.4 19.7 - - + -
271C PRO* 5.1 2.2 - - + +
273C PHE* 3.6 28.9 - - + -
279C ILE* 5.9 0.7 - - + -
312C PHE* 3.4 43.3 + - + +
313C ALA 3.5 3.4 + - - +
315C GLU* 1.3 80.4 - - + +
317C TYR* 1.3 67.3 + - - +
318C PRO* 3.3 6.1 - - - +
321C PHE* 3.9 12.3 - - + -
347C ILE* 4.7 7.4 - - + +
348C ASP* 3.8 40.1 - - + +
350C LEU* 5.9 1.2 - - - +
366C PHE* 4.9 11.2 - - + -
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Residues in contact with TYR 317 (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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313C ALA 3.1 21.1 + - - +
314C LYS* 4.2 11.9 - - - +
315C GLU 3.3 1.4 - - - -
316C ILE* 1.3 77.8 - - - +
318C PRO* 1.3 81.7 - - + +
320C GLN* 3.4 23.4 + - - +
321C PHE 4.9 0.5 + - - -
366C PHE* 3.9 31.0 + + + -
380C CYS* 2.5 48.1 + - - -
383C VAL* 3.9 18.4 + - + +
384C ARG* 3.7 36.1 - - + -
387C ILE* 3.8 28.5 - - + -
409C PRO* 5.6 0.9 - - + -
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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