Contacts of the helix formed by residues 302 - 318 (chain B) 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 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PHE* 2.8 31.0 + - - +
299B LEU 3.3 7.0 + - - +
300B LEU 3.3 0.2 - - - -
301B LYS* 1.3 89.2 + - - +
303B PRO* 1.4 69.8 - - - +
304B GLU* 3.3 6.1 - - + -
305B ALA* 2.9 24.9 + - + +
306B LEU 3.1 9.9 + - - -
404B PHE* 4.0 27.2 - - + +
473B ILE* 5.7 2.0 - - - +
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Residues in contact with PRO 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LEU 4.7 0.4 - - - +
300B LEU 4.9 4.2 - - - +
301B LYS 3.9 7.0 - - - +
302B ASN* 1.4 84.0 - - - +
304B GLU* 1.3 57.5 + - - +
306B LEU* 3.3 9.5 + - + +
307B ALA* 2.9 31.3 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ASN* 4.9 4.5 - - + +
303B PRO* 1.3 79.6 - - + +
305B ALA* 1.3 59.9 + - + +
307B ALA* 3.7 6.3 + - - +
308B ALA* 3.1 27.9 + - - +
406B TYR* 4.0 28.1 + - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.1 10.5 - - + -
302B ASN* 2.9 22.8 + - + +
304B GLU* 1.3 78.9 - - + +
306B LEU* 1.3 65.6 + - - +
308B ALA* 3.1 4.7 + - - +
309B VAL* 3.0 25.1 + - - +
404B PHE* 4.1 9.0 - - + -
406B TYR* 3.5 40.9 - - + -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.3 43.1 + - + +
300B LEU* 4.6 14.6 - - + +
302B ASN 3.1 3.0 + - - +
303B PRO* 3.7 10.3 - - + +
305B ALA* 1.3 77.0 - - - +
307B ALA* 1.3 52.5 + - - +
309B VAL* 3.3 1.7 + - - +
310B ARG* 2.8 79.0 + - + +
459B LEU* 4.0 27.1 - - + -
464B LEU 5.8 0.9 - - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PRO 2.9 18.2 + - - +
304B GLU* 3.9 7.2 - - - +
306B LEU* 1.3 76.6 - - - +
308B ALA* 1.3 53.3 + - - +
310B ARG* 3.7 8.9 - - - +
311B GLY* 2.7 32.4 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU 3.1 19.0 + - - +
305B ALA 3.1 4.9 + - - +
307B ALA* 1.3 74.3 - - - +
309B VAL* 1.3 63.5 + - - +
311B GLY* 3.5 1.5 + - - -
312B GLU* 3.1 24.3 + - - +
340B VAL* 4.0 14.2 - - + +
406B TYR* 3.7 29.2 - - + +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.9 14.6 - - + -
305B ALA 3.0 16.5 + - - +
306B LEU 3.6 6.3 - - - +
308B ALA* 1.3 73.5 - - - +
310B ARG* 1.3 64.6 + - - +
312B GLU* 3.1 7.2 + - - +
313B LEU* 2.9 32.9 + - + +
340B VAL* 4.3 9.6 - - + -
341B LEU* 4.3 24.2 - - + -
344B VAL* 3.8 30.1 - - + -
455B VAL* 4.5 0.7 - - + -
459B LEU* 3.5 28.3 - - + -
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 5.9 0.4 - - - +
306B LEU* 2.8 59.3 + - + +
307B ALA* 3.7 8.3 - - - +
309B VAL* 1.3 72.5 - - - +
311B GLY* 1.3 61.6 + - - +
313B LEU* 4.0 7.5 - - - +
314B GLU* 3.2 38.6 + - - +
459B LEU* 2.8 54.2 + - + +
462B LEU 5.0 2.6 + - - -
463B ASP* 5.7 1.6 - - - +
464B LEU* 4.3 20.4 + - - +
499B ARG* 4.4 4.8 - - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 2.7 20.9 + - - -
308B ALA* 3.8 2.5 - - - -
309B VAL 3.2 0.2 - - - -
310B ARG* 1.3 74.8 - - - +
312B GLU* 1.3 56.1 + - - +
314B GLU* 3.7 2.6 + - - +
315B SER* 2.9 32.6 + - - -
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 3.1 16.9 + - - +
309B VAL* 3.7 4.9 - - - +
311B GLY* 1.3 74.7 - - - +
313B LEU* 1.3 65.8 + - + +
315B SER* 3.4 7.3 + - - -
316B ILE* 3.3 24.2 + - + +
337B SER 4.4 3.8 - - - +
338B THR* 3.2 32.5 - - + -
339B PRO* 3.1 15.4 - - - +
340B VAL* 2.9 32.8 + - + +
341B LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B VAL* 2.9 23.3 + - + +
310B ARG* 4.0 5.2 - - - +
312B GLU* 1.3 77.5 - - + +
314B GLU* 1.3 62.1 + - - +
316B ILE* 3.6 6.9 + - + +
317B LEU* 3.3 24.6 + - - +
334B VAL* 4.9 5.3 - - + +
338B THR* 4.2 21.8 - - + -
341B LEU* 4.4 12.3 - - + -
455B VAL* 4.4 1.3 - - + +
456B PHE* 3.7 41.8 - - + +
459B LEU* 3.8 40.2 - - + -
460B VAL* 4.2 17.0 - - + -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG* 3.2 26.4 + - - +
311B GLY* 4.3 2.2 - - - +
313B LEU* 1.3 74.7 - - - +
315B SER* 1.3 65.0 + - - +
316B ILE 3.1 2.2 - - - -
317B LEU* 3.0 18.9 + - + +
318B TRP* 3.0 48.2 + - + +
459B LEU 5.0 2.9 - - - +
460B VAL* 4.3 23.6 - - + +
499B ARG* 5.1 6.8 + - - -
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLY 2.9 22.9 + - - -
312B GLU* 3.6 9.7 - - - -
314B GLU* 1.3 75.2 - - - +
316B ILE* 1.3 61.8 + - - +
318B TRP* 3.8 18.8 - - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B GLU* 3.3 14.9 + - + +
313B LEU* 3.9 5.8 - - + +
314B GLU 3.1 0.8 - - - -
315B SER* 1.3 76.5 - - - +
317B LEU* 1.3 67.2 + - - +
318B TRP 3.3 2.3 + - - +
331B PRO* 5.4 2.2 - - + +
333B LYS* 2.9 78.4 + - + +
334B VAL* 4.4 11.2 - - + +
337B SER* 2.7 36.1 - - - +
338B THR* 3.6 15.7 - - + -
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU 3.3 9.3 + - - +
314B GLU* 3.0 17.0 + - + +
316B ILE* 1.3 80.2 - - + +
318B TRP* 1.3 88.2 + - + +
331B PRO* 6.5 0.4 - - + -
333B LYS* 5.3 0.3 + - - -
456B PHE* 3.5 38.4 - - + -
460B VAL* 4.3 15.3 - - + -
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Residues in contact with TRP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU* 3.0 54.3 + - + +
315B SER* 3.8 15.6 - - - +
316B ILE 3.3 12.5 - - - +
317B LEU* 1.3 99.5 - - + +
333B LYS* 3.8 10.7 + - - -
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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