Contacts of the helix formed by residues 305 - 321 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A THR 5.9 2.0 - - - +
303A TYR 3.3 4.5 + - - +
304A PRO* 1.3 75.6 - - - +
306A GLN* 1.3 65.0 + - - +
307A GLU* 3.1 24.2 + - - +
308A GLN* 2.9 35.5 + - - +
309A GLN* 2.9 21.9 + - - +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 1.3 74.0 - - - +
307A GLU* 1.3 69.7 + - - +
309A GLN* 3.6 11.3 + - - +
310A LEU* 3.0 28.6 + - - +
339A LEU* 4.3 29.6 - - + +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 3.1 22.1 + - - +
306A GLN* 1.3 91.9 + - - +
308A GLN* 1.3 61.7 + - + +
310A LEU* 3.4 7.1 + - - +
311A HIS* 3.0 28.4 + - - +
314A ARG* 4.8 2.8 + - - -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 3.6 35.1 + - - +
164A SER* 5.1 1.7 + - - -
281A PHE* 5.5 0.2 - - - -
284A TRP* 3.6 23.8 - - + -
303A TYR 4.3 1.4 - - - +
304A PRO* 3.4 18.8 - - + +
305A THR* 2.9 41.9 + - - +
307A GLU* 1.3 82.0 - - + +
309A GLN* 1.3 60.7 + - - +
311A HIS* 3.4 9.5 + - - +
312A PHE* 3.1 22.7 + - - +
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.6 35.1 - - + -
303A TYR* 3.5 18.8 - - - -
304A PRO* 2.7 32.0 + - + -
305A THR 2.9 20.0 + - - +
306A GLN* 3.8 5.3 - - - +
308A GLN* 1.3 72.5 - - - +
310A LEU* 1.3 61.8 + - - +
312A PHE* 3.3 1.9 + - - +
313A ILE* 2.8 36.1 + - - +
339A LEU* 3.2 31.5 - - + +
342A VAL* 5.3 2.6 - - - +
343A SER* 5.7 3.3 - - - -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN 3.0 19.2 + - - +
307A GLU* 3.7 7.6 - - - +
308A GLN 3.3 0.2 - - - -
309A GLN* 1.3 77.6 - - - +
311A HIS* 1.3 53.1 + - - +
313A ILE* 4.3 4.5 - - + -
314A ARG* 2.8 63.2 + - - +
332A ARG* 6.3 0.2 - - - -
335A GLU* 3.6 43.1 - - + +
339A LEU* 3.9 22.8 - - + +
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Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PRO* 2.6 51.8 + - + +
164A SER* 4.3 13.5 - - - -
165A ALA* 4.0 5.8 - - + +
307A GLU 3.0 14.7 + - - +
308A GLN* 3.4 12.1 - - - +
310A LEU* 1.3 74.6 - - - +
312A PHE* 1.3 63.2 + - - +
314A ARG* 3.5 15.9 + - - +
315A HIS* 3.1 55.4 + + - -
1013A UNX 3.8 11.4 - - - -
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Residues in contact with PHE 312 (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 SER* 3.5 31.9 - - - +
167A ILE* 4.0 3.8 - - + -
168A ALA* 3.4 38.7 - - + +
171A MSE 3.6 24.5 - - + -
277A ILE* 3.8 28.3 - - + -
280A HIS* 3.6 23.6 - + - -
281A PHE* 3.6 25.8 - + + -
284A TRP* 5.7 0.7 - + + -
308A GLN 3.1 10.6 + - - +
309A GLN 3.6 6.5 - - - +
311A HIS* 1.3 82.4 - - - +
313A ILE* 1.3 60.9 + - - +
315A HIS* 3.3 3.4 + - - -
316A TYR* 2.9 30.8 + - + -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 4.9 3.6 - - + -
281A PHE* 4.7 10.1 - - + -
309A GLN* 2.8 23.0 + - + +
310A LEU* 3.8 6.1 - - + +
312A PHE* 1.3 75.3 - - + +
314A ARG* 1.3 57.4 + - - +
316A TYR* 3.3 7.1 + - - +
317A LEU* 2.9 40.6 + - + +
335A GLU* 4.1 15.0 - - + +
338A LEU* 3.7 35.4 - - + +
339A LEU* 3.6 50.9 - - + +
342A VAL* 4.5 9.4 - - + -
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Residues in contact with ARG 314 (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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307A GLU 4.8 2.2 + - - -
310A LEU* 2.8 53.1 + - + +
311A HIS* 3.7 27.2 + - - +
312A PHE 3.3 0.2 - - - -
313A ILE* 1.3 74.8 - - - +
315A HIS* 1.3 62.0 + - + +
317A LEU* 3.9 4.7 - - - +
318A ALA* 3.0 27.2 + - - +
331A GLN* 6.1 1.3 - - - +
332A ARG* 4.9 10.3 - - - +
335A GLU* 3.3 32.9 + - + +
1013A UNX 3.5 23.5 - - - -
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Residues in contact with HIS 315 (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 ALA* 3.4 39.2 - - + +
168A ALA* 4.2 2.0 - - + -
169A THR* 3.8 16.0 + - - +
311A HIS* 3.1 44.6 + + - +
312A PHE 3.3 6.7 + - - +
314A ARG* 1.3 77.8 - - + +
316A TYR* 1.3 66.1 + - - +
318A ALA* 3.6 9.1 - - + +
319A GLU* 3.4 15.8 + - - +
1013A UNX 3.8 16.8 - - - -
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Residues in contact with TYR 316 (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 ALA* 3.6 28.6 - - + +
171A MSE 4.3 8.5 - - - -
172A ALA* 3.6 24.7 - - + +
175A HIS* 2.6 42.9 + + - +
237A VAL* 4.9 1.7 - - - +
273A ARG* 3.3 36.4 + - - +
277A ILE* 4.2 16.6 - - + -
312A PHE* 2.9 23.4 + + + +
313A ILE* 3.5 9.0 - - - +
315A HIS* 1.3 78.5 - - - +
317A LEU* 1.3 62.5 + - + +
319A GLU 3.4 0.3 + - - -
320A ALA* 2.9 40.7 + - + +
338A LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 4.4 12.6 - - - +
313A ILE* 2.9 35.1 + - + +
314A ARG* 4.1 3.6 - - - +
316A TYR* 1.3 79.6 - - + +
318A ALA* 1.3 59.5 + - - +
320A ALA* 4.0 4.7 - - + -
321A LYS* 2.8 56.6 + - + +
331A GLN* 4.9 3.6 - - + +
334A LEU* 3.9 32.3 - - + +
335A GLU* 4.0 17.3 - - + +
338A LEU* 3.6 22.4 - - + -
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Residues in contact with ALA 318 (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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314A ARG 3.0 19.1 + - - +
315A HIS* 3.6 13.7 - - + +
317A LEU* 1.3 76.6 - - - +
319A GLU* 1.3 58.4 + - - +
321A LYS 4.0 0.9 - - - -
322A LYS* 3.3 24.9 + - - +
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Residues in contact with GLU 319 (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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169A THR* 3.6 30.6 - - + +
172A ALA* 3.6 24.9 - - + -
173A GLN* 3.6 28.1 + - + +
315A HIS 3.4 7.9 + - - +
316A TYR 3.4 3.2 + - - +
318A ALA* 1.3 78.4 - - - +
320A ALA* 1.3 65.5 + - - +
321A LYS 3.2 0.2 - - - -
322A LYS* 3.2 28.9 + - - +
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Residues in contact with ALA 320 (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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172A ALA* 3.9 9.5 - - + +
273A ARG* 5.6 2.2 - - - +
316A TYR* 2.9 40.3 + - + +
317A LEU* 3.4 12.1 + - + +
319A GLU* 1.3 73.8 - - - +
321A LYS* 1.3 70.1 + - + +
322A LYS 3.4 0.6 + - - -
324A GLU* 4.5 2.6 - - - +
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Residues in contact with LYS 321 (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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273A ARG* 5.2 8.9 - - - +
317A LEU* 2.8 40.7 + - + +
318A ALA* 4.0 2.9 - - - -
320A ALA* 1.3 81.9 - - + +
322A LYS* 1.3 67.2 + - - +
323A GLY 3.4 0.3 + - - -
324A GLU* 3.1 51.1 + - - +
326A LEU* 4.3 17.9 - - + -
334A LEU* 4.3 26.9 - - + +
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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