Contacts of the helix formed by residues 302 - 318 (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 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 4.1 1.1 - - - +
300A LEU 4.8 5.2 - - - +
301A LYS 3.4 9.0 - - - +
302A ASN* 1.3 88.0 - - - +
304A GLU* 1.3 56.4 + - - +
306A LEU* 3.5 9.1 + - + +
307A ALA* 3.0 30.0 + - - +
131B ARG* 3.7 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 3.3 1.4 - - + -
303A PRO* 1.3 74.9 - - - +
305A ALA* 1.3 66.7 + - - +
307A ALA* 3.5 6.0 + - - +
308A ALA* 3.2 23.4 + - - +
406A TYR* 3.6 31.2 + - + -
407A ASN* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.9 14.1 - - + -
302A ASN* 2.9 25.7 + - + +
304A GLU* 1.3 77.0 - - - +
306A LEU* 1.3 64.9 + - - +
308A ALA* 3.5 3.1 + - - +
309A VAL* 3.1 26.5 + - - +
404A PHE* 3.9 3.4 - - + -
406A TYR* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.5 40.0 - - + +
300A LEU* 4.3 22.0 - - + +
302A ASN 3.0 5.9 + - - -
303A PRO* 3.8 10.5 - - + +
304A GLU 3.4 0.2 - - - -
305A ALA* 1.3 76.1 - - - +
307A ALA* 1.3 58.2 + - - +
309A VAL* 3.2 1.7 + - - +
310A ARG* 2.8 71.3 + - + +
459A LEU* 3.9 25.4 - - + -
131B ARG* 6.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO 3.0 18.0 + - - +
304A GLU* 3.9 7.4 - - - +
305A ALA 3.3 0.2 - - - -
306A LEU* 1.3 75.8 - - - +
308A ALA* 1.3 58.0 + - - +
310A ARG* 3.5 10.2 + - - +
311A GLY* 2.9 27.0 + - - -
126B LEU* 4.8 2.3 - - - +
131B ARG* 6.1 2.5 - - - +
254B LYS* 6.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU 3.2 17.8 + - - +
305A ALA 3.8 2.0 - - - +
306A LEU 3.3 0.2 - - - -
307A ALA* 1.3 74.5 - - - +
309A VAL* 1.3 64.5 + - - +
311A GLY* 3.9 1.2 - - - -
312A GLU* 3.1 23.7 + - - +
340A VAL* 4.0 14.1 - - + +
406A TYR* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.9 18.4 - - + -
305A ALA 3.1 15.5 + - - +
306A LEU 3.2 5.6 + - - +
308A ALA* 1.3 73.3 - - - +
310A ARG* 1.3 65.0 + - - +
312A GLU* 3.2 5.8 + - - +
313A LEU* 3.1 33.4 + - + +
340A VAL* 4.0 9.6 - - + -
341A LEU* 4.5 20.2 - - + -
344A VAL* 3.6 31.0 - - + -
455A VAL* 4.5 0.9 - - + -
459A LEU* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 2.8 64.9 + - + +
307A ALA* 3.7 7.6 - - - +
309A VAL* 1.3 73.7 - - - +
311A GLY* 1.3 57.7 + - - +
313A LEU* 3.4 4.3 + - - +
314A GLU* 2.9 34.7 + - - +
459A LEU* 3.0 52.7 + - + +
462A LEU 4.3 4.6 + - - -
464A LEU 5.8 4.4 + - - +
126B LEU* 3.7 18.6 - - + +
130B HIS* 3.1 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 2.9 18.7 + - - -
308A ALA* 3.9 1.8 - - - -
309A VAL 3.2 0.2 - - - -
310A ARG* 1.3 75.0 - - - +
312A GLU* 1.3 61.7 + - - +
314A GLU* 3.4 1.4 + - - +
315A SER* 3.1 29.3 + - - -
122B ALA* 5.2 0.5 - - - +
126B LEU* 3.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 3.1 17.7 + - - +
309A VAL* 3.6 4.9 - - - +
311A GLY* 1.3 76.9 - - - +
313A LEU* 1.3 64.5 + - - +
314A GLU 3.4 0.5 + - - -
315A SER* 3.6 5.0 + - - -
316A ILE* 3.4 26.7 + - + +
337A SER 4.7 1.1 - - - +
338A THR* 3.3 31.0 - - + +
339A PRO* 3.2 13.9 - - + +
340A VAL* 2.8 36.2 + - + +
341A LEU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 3.1 33.0 + - + +
310A ARG* 3.9 4.3 - - - +
312A GLU* 1.3 79.2 - - + +
314A GLU* 1.3 58.1 + - - +
316A ILE* 3.6 7.0 + - - +
317A LEU* 3.0 27.0 + - - +
334A VAL* 4.0 21.3 - - + -
338A THR* 3.8 27.1 - - + -
341A LEU* 4.2 10.5 - - + -
455A VAL* 4.6 4.3 - - + -
456A PHE* 4.1 38.7 - - + +
459A LEU* 4.2 16.2 - - + -
460A VAL* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ARG* 2.9 18.7 + - - +
311A GLY 3.7 3.8 - - - +
313A LEU* 1.3 74.3 - - - +
315A SER* 1.3 59.9 + - - +
317A LEU* 3.1 22.0 + - - +
318A TRP* 2.9 61.2 + - + +
459A LEU 5.4 2.1 - - - +
460A VAL* 4.7 13.2 - - - +
122B ALA* 3.8 21.3 - - + +
125B LYS* 4.7 9.6 - - + +
126B LEU* 3.8 26.7 - - + +
129B LEU* 5.9 1.0 - - - +
130B HIS* 5.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLY 3.1 17.1 + - - -
312A GLU* 3.9 6.7 - - - -
314A GLU* 1.3 75.3 - - - +
316A ILE* 1.3 58.7 + - - +
318A TRP* 3.6 3.1 + - - +
319A GLN* 3.0 28.1 + - - +
118B SER* 5.3 0.9 + - - -
119B ASP* 3.7 27.5 + - - +
122B ALA* 3.8 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.4 20.7 + - + +
313A LEU* 3.7 8.5 - - - +
314A GLU 3.2 0.4 - - - -
315A SER* 1.3 77.2 - - - +
317A LEU* 1.3 57.1 + - - +
319A GLN* 2.7 28.3 + - - +
331A PRO* 4.1 12.2 - - + +
333A LYS* 3.3 48.5 + - + +
334A VAL* 4.0 19.1 - - + +
337A SER* 3.5 24.9 - - - +
338A THR* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU 3.0 15.2 + - - +
314A GLU* 3.4 29.8 - - - +
316A ILE* 1.3 76.7 - - - +
318A TRP* 1.3 63.8 + - + +
319A GLN* 3.2 16.6 + - - -
331A PRO* 4.9 11.4 - - + -
456A PHE* 4.3 27.4 - - + -
460A VAL* 4.1 21.5 - - + -
438B HIS* 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 2.9 48.2 + - - +
315A SER 4.0 3.4 - - - +
317A LEU* 1.3 79.1 - - + +
319A GLN* 1.3 69.5 + - - +
88B TRP* 5.9 0.4 - + - -
96B PHE* 5.9 2.2 - + - -
118B SER* 3.4 37.3 - - - +
121B LYS* 3.6 33.1 + - + -
122B ALA* 3.6 18.1 - - + +
125B LYS* 4.7 10.5 - - - +
438B HIS* 3.1 61.3 + + + -
440B HIS* 3.6 35.2 - + - -
442B LEU* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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