Contacts of the helix formed by residues 289 - 310 (chain C) in PDB entry 1IRI
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 GLY 289 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ARG* 3.2 23.8 - - - +
285C ALA 2.9 18.2 + - - +
288C VAL* 1.3 83.2 - - - +
290C PHE* 1.3 62.0 + - - -
291C ASP* 3.2 3.6 - - - -
292C ASN* 3.1 3.8 + - - +
293C PHE* 3.0 24.4 + - - +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ARG* 6.1 0.2 - - - -
126C LEU* 3.5 45.5 - - + -
129C MET* 4.0 10.8 - - + -
130C LYS* 3.5 50.9 - - + +
133C CYS* 4.5 10.9 - - + +
137C ARG* 5.1 0.2 - - - +
285C ALA* 3.6 14.1 + - + -
289C GLY* 1.3 69.6 - - - -
291C ASP* 1.3 64.5 + - - +
293C PHE* 3.4 25.9 - + - +
294C GLU* 2.7 62.0 + - + +
297C LEU* 5.7 0.2 - - + -
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Residues in contact with ASP 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LYS* 4.5 12.6 + - - -
289C GLY* 3.2 1.0 - - - -
290C PHE* 1.3 78.5 - - - +
292C ASN* 1.3 59.7 + - - +
294C GLU* 3.1 18.6 + - - +
295C GLN* 2.9 30.9 + - - +
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Residues in contact with ASN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 5.6 0.6 - - - +
174C TYR* 3.7 25.9 - - - +
288C VAL* 2.8 38.7 + - + +
289C GLY 3.1 2.9 + - - +
291C ASP* 1.3 81.8 - - - +
293C PHE* 1.3 57.5 + - - +
295C GLN* 3.0 14.3 + - - +
296C LEU* 2.9 24.4 + - - +
484C PRO* 3.7 31.7 - - + +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 4.2 16.4 - - + -
129C MET* 3.9 19.3 - - + -
276C LEU 3.8 22.4 - - - -
277C TRP 3.9 13.5 - - - -
278C SER 4.1 5.8 - - - -
281C GLY* 4.1 9.2 - - - -
284C ILE* 3.9 18.6 - - + -
285C ALA* 3.9 17.7 - - + +
288C VAL* 4.6 1.0 - - - +
289C GLY 3.0 13.3 + - - +
290C PHE* 3.1 26.9 + + - +
292C ASN* 1.3 74.1 - - - +
294C GLU* 1.3 65.7 + - - +
296C LEU* 3.0 34.6 + - + +
297C LEU* 3.0 35.1 + - + +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ARG* 3.0 33.8 + - - +
130C LYS* 4.9 8.0 + - - +
290C PHE* 2.7 47.7 + - + +
291C ASP* 3.4 22.0 - - - +
293C PHE* 1.3 71.9 - - - +
295C GLN* 1.3 67.2 + - + +
297C LEU* 3.1 12.7 + - + +
298C SER* 2.9 25.2 + - - +
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Residues in contact with GLN 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C HIS* 4.9 12.3 + - - -
291C ASP* 2.9 17.3 + - + +
292C ASN* 3.0 17.0 + - - +
294C GLU* 1.3 79.7 - - - +
296C LEU* 1.3 63.0 + - - +
298C SER* 3.0 20.9 + - - -
299C GLY 3.0 10.6 + - - -
484C PRO* 4.1 13.2 - - + -
485C PHE* 3.7 38.5 - - - +
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Residues in contact with LEU 296 (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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167C VAL* 4.2 20.9 - - + -
171C LEU* 4.6 3.6 - - + -
276C LEU* 3.8 21.8 - - + -
277C TRP* 3.8 12.9 - - + -
284C ILE* 4.4 2.7 - - + -
292C ASN 2.9 11.6 + - - +
293C PHE* 3.1 38.1 - - + +
295C GLN* 1.3 76.7 - - - +
297C LEU* 1.3 60.8 + - - +
299C GLY 3.4 0.5 + - - -
300C ALA 3.3 15.6 + - - -
484C PRO* 3.5 24.3 + - + +
487C LEU* 4.3 18.6 - - + -
488C GLY* 3.4 29.5 - - - +
491C VAL* 5.9 0.7 - - + -
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Residues in contact with LEU 297 (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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103C LEU 4.0 9.0 - - - +
104C ARG* 3.4 24.2 - - + +
106C ARG* 3.8 32.8 - - - +
126C LEU* 4.0 24.2 - - + -
277C TRP* 3.6 39.9 - - + +
293C PHE* 3.0 31.0 + - + +
294C GLU* 3.1 13.0 + - + +
296C LEU* 1.3 74.8 - - - +
298C SER* 1.3 53.2 + - - +
300C ALA 3.2 1.4 + - - +
301C HIS* 2.8 34.7 + - - +
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ARG* 3.8 25.0 + - - +
294C GLU* 2.9 15.9 + - - +
295C GLN* 3.4 16.8 + - - -
297C LEU* 1.3 73.8 - - - +
299C GLY* 1.3 60.1 + - - +
301C HIS* 3.5 2.8 - - - +
302C TRP* 2.7 30.0 + - - +
485C PHE* 3.7 16.7 - - - -
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Residues in contact with GLY 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLN 3.0 10.5 + - - -
296C LEU 3.9 0.9 - - - -
297C LEU 3.2 0.2 - - - -
298C SER* 1.3 74.2 - - - +
300C ALA* 1.3 67.8 + - - +
302C TRP* 3.1 3.8 + - - +
303C MET 3.0 15.8 + - - -
485C PHE* 3.3 41.4 - - - -
489C ALA* 3.4 15.9 - - - +
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 3.5 24.7 - - - +
277C TRP* 3.5 26.9 - - + -
296C LEU 3.3 4.9 + - - -
297C LEU 3.2 6.5 + - - +
299C GLY* 1.3 74.7 - - - +
301C HIS* 1.3 58.0 + - - +
303C MET* 2.9 7.8 + - - +
304C ASP* 2.8 31.2 + - - +
488C GLY 3.2 20.2 - - - +
492C ALA* 3.8 7.1 - - + +
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Residues in contact with HIS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL 5.1 1.0 + - - -
104C ARG* 3.0 26.1 + - - +
105C ASN* 3.6 22.0 - - - -
106C ARG* 3.8 23.1 - - + -
107C SER* 2.9 29.0 + - - -
297C LEU 2.8 12.0 + - - +
298C SER* 3.5 5.6 - - - +
300C ALA* 1.3 76.6 - - - +
302C TRP* 1.3 64.1 + - - +
304C ASP* 3.4 12.8 + - - +
305C GLN* 3.2 53.4 + - + +
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Residues in contact with TRP 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 4.0 22.9 - - + -
45C ASN 3.4 19.9 + - - -
46C THR* 3.7 45.7 + - + +
47C ASN* 5.8 1.4 - - - +
48C HIS* 6.0 0.2 - + - -
51C ILE* 4.9 0.2 - - + -
298C SER 2.7 17.6 + - - +
299C GLY 3.4 9.4 - - - +
301C HIS* 1.3 75.8 - - - +
303C MET* 1.3 87.5 + - + +
305C GLN* 3.0 13.5 + - + +
306C HIS* 3.0 45.9 + + + -
485C PHE* 3.8 15.9 - + + -
489C ALA* 4.8 2.0 - - + -
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Residues in contact with MET 303 (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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44C LEU* 4.8 4.7 - - + -
51C ILE* 4.1 13.2 - - + -
299C GLY 3.0 9.3 + - - +
300C ALA 2.9 8.5 + - - +
302C TRP* 1.3 96.1 - - + +
304C ASP* 1.3 66.6 + - - +
306C HIS* 3.6 23.9 - - - +
307C PHE* 2.9 22.3 + - - +
317C PRO* 4.6 4.9 - - + -
489C ALA* 3.4 37.2 - - + +
490C LEU* 5.3 0.2 - - - -
492C ALA* 4.0 7.2 - - + +
493C MET* 3.6 40.4 - - + +
496C HIS* 4.7 4.5 - - + -
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Residues in contact with ASP 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 3.9 16.2 - - + -
101C VAL* 3.7 16.4 - - - +
104C ARG* 2.7 45.5 + - - +
300C ALA 2.8 14.1 + - - +
301C HIS* 3.4 12.9 + - - +
303C MET* 1.3 77.1 - - - +
305C GLN* 1.3 66.5 + - - +
307C PHE* 3.4 3.1 + - - +
308C ARG* 3.0 29.2 + - - +
492C ALA* 4.3 0.5 - - - +
496C HIS* 2.8 28.5 + - - -
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Residues in contact with GLN 305 (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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85C PHE* 5.0 6.3 - - - -
107C SER* 5.6 0.2 - - - -
301C HIS* 3.2 46.0 + - + +
302C TRP* 3.0 11.9 + - + +
304C ASP* 1.3 81.4 - - - +
306C HIS* 1.3 69.9 - - - +
308C ARG* 3.0 14.7 + - - +
309C THR* 3.0 35.8 + - + +
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Residues in contact with HIS 306 (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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44C LEU* 3.6 31.1 - - + +
302C TRP* 3.0 37.4 + + + -
303C MET* 3.3 18.1 + - - +
305C GLN* 1.3 80.7 - - - +
307C PHE* 1.3 66.4 + - - +
308C ARG 3.0 0.2 + - - -
309C THR* 4.5 2.0 - - - -
310C THR* 2.9 56.0 + - + -
314C LYS 4.1 2.9 - - - -
315C ASN* 3.9 3.6 - - - -
316C ALA* 3.1 28.7 + - + +
317C PRO* 3.9 17.7 - - + -
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Residues in contact with PHE 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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77C VAL* 5.2 3.6 - - + -
81C ARG* 3.1 49.0 + - + -
84C MET* 4.8 0.2 - - + -
85C PHE* 4.1 8.1 - + - -
303C MET 2.9 17.0 + - - +
304C ASP 3.5 3.1 - - - +
306C HIS* 1.3 75.7 - - - +
308C ARG* 1.3 58.2 + - - +
315C ASN* 2.6 40.2 + - - +
317C PRO* 3.7 11.0 - - + -
318C VAL* 3.8 11.0 - - + -
496C HIS* 3.4 46.7 - + + -
499C PHE* 3.8 25.4 - + - -
500C VAL* 3.7 24.5 - - + -
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Residues in contact with ARG 308 (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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81C ARG* 3.5 36.9 + - - +
82C GLU* 2.6 33.7 + - - +
85C PHE* 3.6 48.7 + - + +
86C ASN* 4.1 16.2 + - - +
304C ASP 3.0 17.1 + - - +
305C GLN* 3.0 17.3 + - - +
307C PHE* 1.3 79.3 - - - +
309C THR* 1.3 66.7 + - + +
310C THR 3.6 0.4 - - - -
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Residues in contact with THR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C GLN* 3.0 28.7 + - + +
306C HIS* 4.0 2.1 + - - -
308C ARG* 1.3 88.6 - - + +
310C THR* 1.3 64.9 + - - +
311C PRO* 3.8 6.9 - - - +
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Residues in contact with THR 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 5.5 1.2 - - - +
81C ARG* 4.8 4.5 + - - -
306C HIS* 2.9 42.6 + - + -
307C PHE 4.5 0.7 - - - +
308C ARG 3.6 0.8 - - - -
309C THR* 1.3 81.6 + - - +
311C PRO* 1.3 78.6 - - + +
312C LEU 3.2 2.3 + - - -
314C LYS* 3.4 39.0 - - + +
315C ASN* 3.4 20.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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