Contacts of the helix formed by residues 305 - 321 (chain B) in PDB entry 2IG7
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 THR 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR 3.4 4.2 + - - +
304B PRO* 1.3 75.5 - - - +
306B GLN* 1.3 60.4 + - - +
307B GLU* 3.3 8.6 + - - +
308B GLN* 2.8 44.6 + - - +
309B GLN* 2.8 28.1 + - - +
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 1.3 73.6 - - - +
307B GLU* 1.3 73.4 + - + +
309B GLN* 3.6 10.1 - - - +
310B LEU* 2.9 31.2 + - + +
339B LEU* 4.3 28.0 - - + +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 3.2 7.5 + - - +
306B GLN* 1.3 98.9 + - + +
308B GLN* 1.3 56.6 + - + +
310B LEU* 3.4 25.0 + - - +
311B HIS* 3.0 28.2 + - - +
314B ARG* 4.9 6.2 + - - -
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 3.7 34.4 + - - +
164B SER* 4.9 1.0 + - - -
281B PHE* 5.3 0.4 - - - -
284B TRP* 3.6 29.7 - - + -
303B TYR 4.3 0.7 - - - +
304B PRO* 3.4 9.3 - - + +
305B THR* 2.8 51.8 + - - +
307B GLU* 1.3 73.8 - - + +
309B GLN* 1.3 64.6 + - - +
311B HIS* 3.4 10.0 + - - +
312B PHE* 3.2 21.7 + - - +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.5 38.2 - - + -
303B TYR* 3.4 19.4 + - - -
304B PRO* 3.0 28.5 + - + -
305B THR 2.8 18.2 + - - +
306B GLN* 3.6 3.6 - - - +
308B GLN* 1.3 77.7 - - - +
310B LEU* 1.3 56.5 + - - +
312B PHE* 3.3 4.0 + - - +
313B ILE* 2.9 32.8 + - - +
339B LEU* 3.6 29.3 - - + +
342B VAL* 4.3 8.0 - - - +
343B SER* 5.4 2.1 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLN* 2.9 20.4 + - - +
307B GLU* 3.7 27.1 - - - +
308B GLN 3.4 0.2 - - - -
309B GLN* 1.3 73.8 - - - +
311B HIS* 1.3 60.2 + - - +
313B ILE* 4.1 7.4 - - + -
314B ARG* 2.9 60.9 + - - +
335B GLU* 3.6 39.3 - - + +
339B LEU* 4.1 22.4 - - + +
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO* 2.7 50.3 + - + -
164B SER* 4.3 13.9 - - - -
165B ALA* 3.9 6.7 - - + +
307B GLU 3.0 14.1 + - - +
308B GLN* 3.5 11.7 - - - +
309B GLN 3.3 0.2 - - - -
310B LEU* 1.3 78.1 - - - +
312B PHE* 1.3 64.4 + - - +
314B ARG* 3.5 15.6 + - - +
315B HIS* 3.3 50.1 + - - -
1020B UNX 3.5 16.2 - - - -
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Residues in contact with PHE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.5 32.1 - - - +
167B ILE* 4.1 4.3 - - + -
168B ALA* 3.3 44.8 - - + +
171B MSE 3.5 24.0 - - + -
277B ILE* 3.9 26.9 - - + -
280B HIS* 3.7 22.7 - + - -
281B PHE* 3.6 26.2 - + + -
284B TRP* 5.7 0.4 - + + -
308B GLN 3.2 10.1 + - - +
309B GLN 3.5 7.9 - - - +
311B HIS* 1.3 80.5 - - - +
313B ILE* 1.3 61.5 + - + +
315B HIS* 3.3 3.6 + - - -
316B TYR* 2.9 31.1 + - + -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 5.1 5.4 - - + -
281B PHE* 4.8 5.4 - - + -
309B GLN* 2.9 22.5 + - + +
310B LEU* 3.8 5.8 - - + +
312B PHE* 1.3 83.9 - - + +
314B ARG* 1.3 58.4 + - - +
316B TYR* 3.6 5.9 - - - +
317B LEU* 2.8 50.3 + - + +
335B GLU* 4.0 23.1 - - + +
338B LEU* 4.0 23.6 - - + +
339B LEU* 3.7 45.1 - - + +
342B VAL* 4.7 6.5 - - + -
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 4.9 6.1 + - - -
310B LEU* 2.9 53.7 + - + +
311B HIS* 3.7 23.2 + - - +
312B PHE 3.3 0.2 - - - -
313B ILE* 1.3 76.4 - - - +
315B HIS* 1.3 63.2 + - + +
317B LEU* 3.5 4.3 + - - +
318B ALA* 3.0 28.2 + - - +
335B GLU* 3.5 33.9 + - - +
1020B UNX 3.7 22.6 - - - -
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Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 3.6 36.1 + - + +
168B ALA* 4.1 4.9 - - + -
169B THR* 4.1 10.6 + - - +
311B HIS* 3.3 44.6 - + - +
312B PHE 3.3 6.8 + - - +
314B ARG* 1.3 76.8 - - + +
316B TYR* 1.3 68.1 + - - +
318B ALA* 3.5 9.1 + - - +
319B GLU* 3.3 20.6 + - - +
1020B UNX 3.7 13.2 - - - -
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Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 3.6 27.0 - - + +
171B MSE 4.2 11.7 - - + -
172B ALA* 3.5 22.7 - - + +
175B HIS* 2.6 45.3 + + - +
237B VAL* 5.1 1.4 - - - +
273B ARG* 3.3 38.6 - - + +
277B ILE* 4.3 11.2 - - + -
312B PHE* 2.9 23.6 + + + +
313B ILE* 3.6 8.1 - - - +
315B HIS* 1.3 77.1 - - - +
317B LEU* 1.3 67.9 + - + +
319B GLU 3.2 2.3 + - - -
320B ALA* 2.9 44.0 + - + +
338B LEU* 4.3 8.1 - - + -
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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
----------------------------------------------------------
273B ARG* 4.5 11.4 - - - +
313B ILE* 2.8 38.9 + - + +
314B ARG* 4.1 3.1 - - - +
316B TYR* 1.3 77.8 - - + +
318B ALA* 1.3 58.6 + - - +
320B ALA* 4.2 3.4 - - + -
321B LYS* 2.7 61.2 + - + +
331B GLN* 5.0 7.9 - - - +
334B LEU* 3.8 33.2 - - + +
335B GLU* 4.0 15.0 - - + +
338B LEU* 3.9 21.5 - - + -
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG 3.0 18.6 + - - +
315B HIS* 3.6 12.3 - - - +
317B LEU* 1.3 76.2 - - - +
319B GLU* 1.3 61.0 + - - +
321B LYS* 3.9 1.1 - - - -
322B LYS* 3.3 22.5 + - - +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B THR* 3.5 36.5 - - + +
172B ALA* 3.6 17.5 - - + -
173B GLN* 3.5 30.5 + - + +
315B HIS 3.3 8.0 + - - +
316B TYR 3.2 2.6 + - - +
318B ALA* 1.3 78.4 - - - +
320B ALA* 1.3 65.3 + - - +
322B LYS* 3.2 24.3 + - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA* 4.0 11.4 - - + +
175B HIS* 6.6 0.2 - - + -
273B ARG* 5.7 2.0 - - - +
316B TYR* 2.9 38.7 + - + +
317B LEU* 4.0 7.4 - - + +
319B GLU* 1.3 77.9 - - - +
321B LYS* 1.3 65.7 - - + +
322B LYS 3.3 2.2 + - - -
324B GLU* 4.5 3.8 - - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 5.6 5.3 - - - +
317B LEU* 2.7 41.7 + - + +
318B ALA* 3.9 3.1 - - - -
320B ALA* 1.3 76.9 - - + +
322B LYS* 1.3 65.9 + - - +
323B GLY 3.4 0.3 + - - -
324B GLU* 3.0 52.7 + - - +
326B LEU* 4.2 20.0 - - + -
334B LEU* 4.2 31.2 - - + +
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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