Contacts of the helix formed by residues 287 - 302 (chain A) in PDB entry 2IAG
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 ASN 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A TRP* 6.2 1.4 - - - -
283A ALA 5.2 5.6 + - - +
284A THR 5.4 0.8 - - - -
285A GLN 3.2 0.8 - - - +
286A GLY* 1.3 85.3 - - - +
288A MET* 1.3 59.7 + - - +
289A GLY 3.4 2.0 - - - -
290A PRO* 3.4 4.4 - - - +
291A ALA* 2.9 29.3 + - - +
483A PHE 4.7 4.4 + - - +
484A GLY* 3.8 8.0 - - - -
485A LEU* 2.9 41.1 + - + +
600A HEM 3.4 55.9 + - + +
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 5.4 1.1 - - - -
172A LEU* 3.7 31.7 - - + +
176A GLY* 4.6 1.1 - - - -
284A THR 4.2 9.2 - - - +
285A GLN* 3.4 32.4 + - - +
287A ASN* 1.3 76.9 - - - +
289A GLY* 1.3 64.1 + - - +
291A ALA* 3.2 2.4 + - - +
292A ALA* 2.9 26.3 + - - +
446A TYR* 4.6 11.9 - - + +
447A ALA* 4.1 14.6 - - + +
450A SER* 3.5 30.3 - - - -
451A ILE* 4.2 10.9 - - + +
600A HEM 3.7 34.7 - - + +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A SER* 3.6 16.5 - - - -
169A TYR* 3.7 31.2 - - - -
172A LEU* 4.1 8.0 - - - +
173A LEU 5.6 0.4 - - - +
285A GLN 4.3 4.4 + - - -
288A MET* 1.3 79.4 - - - +
290A PRO* 1.4 69.5 - - - +
292A ALA* 3.3 0.5 + - - +
293A PHE* 3.0 18.9 + - - +
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Residues in contact with PRO 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 4.1 13.5 - - + -
169A TYR* 3.8 34.1 - - + -
286A GLY 3.7 15.3 - - - +
287A ASN 3.4 12.8 - - - +
289A GLY* 1.4 87.6 - - - +
291A ALA* 1.3 60.1 + - - +
293A PHE* 3.3 2.3 + - - +
294A TRP* 2.9 32.3 + - + +
485A LEU* 4.0 9.0 - - + +
486A MET 3.9 20.2 - - - +
487A GLN* 4.1 15.9 - - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ASN 2.9 19.0 + - - +
288A MET 3.5 4.3 - - - +
290A PRO* 1.3 74.4 - - - +
292A ALA* 1.3 63.5 + - - +
294A TRP* 3.3 5.7 + - - +
295A LEU* 3.1 23.2 + - - +
345A LEU* 5.2 2.8 - - + +
348A SER* 4.2 2.9 + - - -
349A LEU* 4.0 11.2 - - + -
352A THR* 5.3 0.4 - - - -
451A ILE* 3.9 10.1 - - + -
485A LEU* 3.9 16.5 - - + +
600A HEM 3.8 22.7 - - + -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A SER* 4.2 2.2 - - - -
172A LEU* 3.4 32.1 - - + -
288A MET 2.9 7.7 + - - +
289A GLY 3.7 2.2 - - - +
291A ALA* 1.3 73.5 - - - +
293A PHE* 1.3 60.2 + - - +
295A LEU* 3.8 6.8 - - - +
296A LEU* 2.9 35.2 + - + +
451A ILE* 4.8 15.4 - - + +
454A PHE* 4.0 18.4 - - + -
455A VAL* 5.5 2.2 - - + -
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.6 24.3 - - + +
165A LEU* 3.2 49.1 - - + -
168A SER* 3.7 14.5 - - - -
289A GLY 3.0 13.2 + - - +
290A PRO 3.4 8.1 - - - +
291A ALA 3.2 0.4 - - - -
292A ALA* 1.3 76.8 - - - +
294A TRP* 1.3 92.9 + + - +
297A LEU* 2.9 48.0 + - + +
474A PRO* 4.8 0.2 - - + -
488A PRO* 3.4 31.4 - - + -
491A ASP* 3.8 8.7 - - - -
492A VAL* 4.2 13.9 - - + -
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Residues in contact with TRP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PRO* 2.9 26.0 + - - +
291A ALA 3.8 4.7 - - - +
293A PHE* 1.3 96.3 - + - +
295A LEU* 1.3 51.8 + - - +
297A LEU* 3.4 12.3 + - + +
298A PHE* 2.8 52.5 + + + -
348A SER* 3.6 3.8 - - - +
352A THR* 3.4 42.6 - - + +
473A ILE* 3.8 24.0 - - + -
474A PRO* 3.8 12.8 - - + -
476A PHE* 3.6 33.0 - + - -
485A LEU* 4.3 3.1 - - + -
486A MET 2.9 22.9 + - - -
487A GLN* 3.9 1.9 - - - +
488A PRO* 3.7 32.7 - - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA 3.1 15.6 + - - +
292A ALA* 3.8 4.7 - - - +
294A TRP* 1.3 76.1 - - - +
296A LEU* 1.3 65.9 + - + +
298A PHE* 3.3 4.9 + - - +
299A LEU* 3.0 49.5 + - + +
341A LEU* 4.6 8.3 - - + -
344A VAL* 3.7 18.6 - - + +
345A LEU* 3.8 43.5 - - + -
348A SER* 3.1 18.2 + - - +
451A ILE* 4.2 14.6 - - + -
455A VAL* 4.0 21.8 - - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.2 18.2 - - + -
167A PHE* 4.3 9.6 - - + -
168A SER* 3.8 20.2 - - - +
292A ALA 2.9 18.2 + - - +
293A PHE 3.9 2.7 - - - +
295A LEU* 1.3 79.0 - - + +
297A LEU* 1.3 58.2 + - - +
299A LEU* 3.3 8.7 + - + +
300A LEU* 2.8 39.2 + - + +
454A PHE* 3.9 20.6 - - + -
455A VAL* 4.6 22.4 - - + -
458A VAL* 4.5 10.3 - - + -
459A LEU* 4.2 24.7 - - + -
464A LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.6 12.9 - - + +
293A PHE* 2.9 36.1 + - + +
294A TRP* 3.6 12.1 - - + +
296A LEU* 1.3 76.0 - - - +
298A PHE* 1.3 56.6 + - + +
300A LEU* 3.2 4.2 + - - +
301A LYS* 2.9 44.5 + - + +
466A LEU* 4.2 13.7 - - + -
471A VAL* 5.2 2.5 - - + -
472A GLU 6.0 0.2 - - - +
473A ILE* 4.0 24.0 - - + -
474A PRO* 3.8 28.5 - - + -
492A VAL* 4.0 26.7 - - + -
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A TRP* 2.8 36.0 + + + +
295A LEU 3.7 4.5 - - - +
297A LEU* 1.3 74.3 - - + +
299A LEU* 1.3 60.7 + - - +
301A LYS* 3.4 1.3 + - - -
302A ASN* 2.7 34.4 + - - +
348A SER* 3.4 22.7 - - - -
351A LEU* 3.8 24.0 - - + -
352A THR* 4.0 27.6 - - + -
404A PHE* 3.6 48.9 - + + -
473A ILE* 3.8 35.0 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU* 3.0 39.2 + - + +
296A LEU* 3.6 15.0 - - + +
297A LEU 3.3 0.2 - - - -
298A PHE* 1.3 73.5 - - - +
300A LEU* 1.3 64.9 + - + +
302A ASN 3.1 22.7 + - - +
303A PRO* 4.1 0.5 - - - +
305A ALA* 3.9 23.3 - - + +
306A LEU* 3.5 31.6 - - + +
309A VAL* 3.9 35.4 - - + -
344A VAL* 3.7 22.0 - - + -
404A PHE* 4.3 3.8 - - + -
455A VAL* 4.9 0.7 - - + -
459A LEU* 4.5 6.5 - - + -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.1 15.5 - - + -
296A LEU* 2.8 26.8 + - + +
297A LEU* 3.6 5.4 - - - +
299A LEU* 1.3 75.9 - - + +
301A LYS* 1.3 60.9 + - - +
302A ASN 3.7 0.2 + - - -
303A PRO* 4.8 5.4 - - - +
306A LEU* 4.3 21.6 - - + +
459A LEU* 6.4 2.0 - - + -
464A LEU* 3.8 50.7 - - + +
465A GLU* 5.1 1.1 - - - -
466A LEU* 4.0 41.1 - - + +
494A VAL* 4.6 4.0 - - + -
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LEU* 2.9 25.8 + - + +
298A PHE* 4.5 1.1 - - - -
299A LEU 3.2 0.2 - - - -
300A LEU* 1.3 76.5 - - - +
302A ASN* 1.3 72.8 + - - +
303A PRO* 3.4 9.5 - - - +
466A LEU* 3.8 19.7 - - + -
469A ALA 3.2 19.7 + - - +
470A ASP* 3.7 6.9 + - - +
471A VAL* 2.5 34.1 + - + +
472A GLU* 4.6 12.9 + - - +
473A ILE* 4.2 25.4 - - + -
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Residues in contact with ASN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PHE* 2.7 29.9 + - - +
299A LEU 3.1 6.8 + - - +
301A LYS* 1.3 91.3 + - - +
303A PRO* 1.3 66.2 - - - +
304A GLU 3.3 2.9 - - - -
305A ALA* 2.9 26.2 + - + +
306A LEU 3.0 10.6 + - - -
404A PHE* 3.5 31.3 - - + +
473A ILE* 5.6 1.8 - - - +
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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