Contacts of the helix formed by residues 443 - 461 (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 GLY 443 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.2 6.1 - - - -
441B CYS* 3.3 8.4 - - - -
442B LEU* 1.3 79.1 - - - +
444B ARG* 1.3 51.7 + - - +
445B SER 3.4 2.5 - - - -
446B TYR* 3.2 7.2 + - - +
447B ALA* 2.7 37.2 + - - +
600B HEM 3.5 36.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 3.6 50.0 + - + +
125B LYS* 6.3 0.4 - - - +
431B ASN 5.8 1.4 + - - -
434B TRP* 3.4 70.6 - - + +
441B CYS* 3.4 15.5 - - + +
442B LEU 3.4 3.6 - - - -
443B GLY* 1.3 76.5 - - - +
445B SER* 1.3 56.8 + - - +
447B ALA* 3.6 0.9 - - - +
448B VAL* 2.9 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ARG* 4.8 3.1 + - - +
500A PRO* 5.5 2.4 - - - +
501A HIS* 3.2 36.6 + - - +
128B LEU 4.6 1.6 - - - -
129B LEU* 4.1 19.5 - - - +
133B LEU* 3.8 27.6 - - - +
442B LEU 5.2 0.6 + - - -
443B GLY 3.4 0.2 - - - -
444B ARG* 1.3 77.9 - - - +
446B TYR* 1.3 57.8 + - - +
448B VAL* 3.5 1.4 + - - +
449B ASN* 3.0 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.9 6.0 + - + +
133B LEU* 3.6 20.0 - - + +
136B LEU* 4.1 38.8 - - + -
137B THR* 4.9 3.6 - - - -
140B MET* 3.5 32.7 - - + +
176B GLY* 3.7 14.4 + - - -
179B THR* 3.7 12.3 - - + +
180B LEU* 4.2 15.6 - - + +
288B MET* 4.3 5.8 - - + +
443B GLY* 3.2 9.4 + - - +
445B SER* 1.3 76.5 - - - +
447B ALA* 1.3 55.2 + - - +
449B ASN* 3.7 3.2 - - + +
450B SER* 2.7 54.8 + - - -
600B HEM 3.7 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B MET* 4.0 11.0 - - - -
434B TRP* 3.8 8.5 - - + -
443B GLY 2.7 19.5 + - - +
444B ARG 3.6 4.7 - - - +
446B TYR* 1.3 73.2 - - - +
448B VAL* 1.3 63.0 + - - +
450B SER* 3.4 1.7 + - - -
451B ILE* 3.0 32.1 + - - +
600B HEM 3.6 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 3.9 33.2 - - + +
342B ASP* 4.7 5.4 - - - +
345B LEU* 4.0 22.4 - - + -
434B TRP* 3.6 25.6 - - + +
444B ARG* 2.9 21.1 + - - +
445B SER 3.9 3.6 - - - +
447B ALA* 1.3 73.9 - - - +
449B ASN* 1.3 69.3 + - - +
451B ILE* 4.0 1.4 - - - +
452B LYS* 3.2 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 5.2 4.8 + - - -
133B LEU* 4.0 13.3 - - - +
137B THR* 3.1 30.1 + - + +
335B LEU* 3.7 40.9 + - + +
445B SER* 3.0 23.0 + - - +
446B TYR* 3.7 5.8 - - + +
448B VAL* 1.3 81.8 - - - +
450B SER* 1.3 59.0 + - - +
452B LYS* 3.3 5.4 + - - +
453B GLN* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.5 19.9 - - - +
144B LEU* 3.7 4.3 - - - +
172B LEU* 3.8 3.0 - - - +
288B MET* 3.6 22.7 - - - -
446B TYR* 2.7 46.4 + - - -
447B ALA 3.7 0.2 - - - -
448B VAL 3.3 0.2 - - - -
449B ASN* 1.3 74.5 - - - +
451B ILE* 1.3 60.3 + - - +
453B GLN* 3.4 12.1 + - - +
454B PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.6 6.1 - - + -
288B MET* 4.2 19.7 - - + +
291B ALA* 3.9 20.0 - - + -
292B ALA* 4.5 12.1 - - + -
295B LEU* 4.3 14.4 - - + -
345B LEU* 4.1 33.0 - - + -
349B LEU* 5.8 0.4 - - + -
434B TRP* 5.4 2.7 - - + -
447B ALA* 3.0 23.2 + - + +
448B VAL* 4.0 3.4 - - - +
450B SER* 1.3 77.2 - - - +
452B LYS* 1.3 60.1 + - + +
454B PHE* 3.3 6.2 + - - +
455B VAL* 2.9 34.0 + - + +
600B HEM 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL* 3.6 15.7 - - + +
335B LEU* 3.0 28.6 + - + +
338B THR* 2.6 22.6 + - - +
341B LEU* 3.6 39.4 - - + +
342B ASP* 2.5 35.6 + - - +
345B LEU* 4.7 9.2 - - + -
448B VAL* 3.2 32.3 + - + +
449B ASN* 3.7 5.8 - - - +
451B ILE* 1.3 77.1 - - + +
453B GLN* 1.3 59.1 - - - +
455B VAL* 3.5 2.9 + - - +
456B PHE* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.1 40.3 + - - +
140B MET* 3.7 27.7 - - - +
141B TYR* 3.3 31.5 + - + +
144B LEU* 3.8 10.1 - - + -
331B PRO* 5.8 4.6 - - + +
334B VAL* 4.7 7.4 - - + -
335B LEU* 4.2 12.6 - - + +
449B ASN* 2.9 20.8 + - - +
450B SER* 3.7 6.2 - - - +
451B ILE 3.3 0.2 - - - -
452B LYS* 1.3 74.3 - - - +
454B PHE* 1.3 65.0 + - - +
456B PHE* 3.4 7.8 + - - +
457B LEU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.7 22.8 - - + +
148B LEU* 3.6 29.4 - - + -
167B PHE* 3.7 23.6 - + - -
168B SER* 4.0 22.0 - - - -
171B PHE* 3.8 11.4 - - + -
172B LEU* 3.8 27.6 - - + -
292B ALA* 4.0 11.0 - - + -
296B LEU* 3.7 24.7 - - + -
450B SER 2.9 18.1 + - - +
451B ILE 3.5 4.9 - - - +
452B LYS 3.3 0.2 - - - -
453B GLN* 1.3 77.6 - - - +
455B VAL* 1.3 63.9 + - + +
457B LEU* 3.3 7.4 + - + +
458B VAL* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 5.6 2.0 - - + -
295B LEU* 3.7 26.9 - - + -
296B LEU* 4.0 16.4 - - + -
299B LEU* 4.9 0.2 - - + -
309B VAL* 4.5 2.5 - - + -
313B LEU* 4.6 1.8 - - + -
341B LEU* 3.9 25.1 - - + -
451B ILE* 2.9 32.9 + - + +
452B LYS* 3.9 7.2 - - - +
454B PHE* 1.3 77.8 - - + +
456B PHE* 1.3 57.8 + - - +
458B VAL* 3.4 5.4 + - - +
459B LEU* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 4.1 29.4 - + - -
313B LEU* 3.7 28.9 - - + -
317B LEU* 3.5 35.2 - - + -
331B PRO* 4.8 11.7 - - + -
334B VAL* 3.7 36.8 - - + -
452B LYS 3.0 19.5 + - - +
453B GLN* 3.5 7.2 - - - +
455B VAL* 1.3 76.7 - - - +
457B LEU* 1.3 60.8 + - - +
460B VAL* 2.9 53.4 + - + +
461B HIS* 4.3 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 4.0 27.8 - - + +
144B LEU* 3.7 32.1 - - + +
145B HIS* 3.8 40.4 - - + +
148B LEU* 5.6 9.2 - - + -
149B LEU* 5.0 4.3 - - + -
453B GLN 3.0 20.5 + - - +
454B PHE* 3.7 9.9 - - + +
456B PHE* 1.3 78.3 - - + +
458B VAL* 1.3 59.3 + - + +
461B HIS* 3.0 52.9 + - + +
462B LEU* 3.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.5 2.9 - - + -
167B PHE* 3.9 17.0 - - + -
296B LEU* 5.1 4.3 - - + -
310B ARG* 5.7 0.3 + - - -
454B PHE* 3.1 48.7 + - + +
455B VAL* 3.9 5.4 - - - +
457B LEU* 1.3 77.4 - - - +
459B LEU* 1.3 64.3 + - + +
462B LEU* 3.0 40.4 + - + +
464B LEU* 3.5 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.8 11.2 - - + -
299B LEU* 4.4 4.3 - - + -
300B LEU* 5.7 4.0 - - + -
306B LEU* 4.0 23.8 - - + -
309B VAL* 3.5 32.3 - - + -
310B ARG* 2.8 42.2 + - + +
313B LEU* 3.8 13.7 - - + -
314B GLU* 5.0 3.1 - - - +
455B VAL* 2.9 30.7 + - + +
458B VAL* 1.3 90.0 - - + +
460B VAL* 1.3 55.0 + - - +
462B LEU 3.8 0.2 - - - +
464B LEU* 5.4 5.6 - - + -
499B ARG* 2.8 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.2 20.2 - - + -
314B GLU* 4.3 16.8 - - + +
317B LEU* 4.3 15.7 - - + -
456B PHE* 2.9 49.0 + - + +
459B LEU* 1.3 78.8 - - - +
461B HIS* 1.3 72.6 - - + +
499B ARG* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 4.2 15.5 + - - -
145B HIS* 4.3 21.8 + + - -
149B LEU* 4.5 13.0 - - + -
456B PHE* 4.3 14.8 - + - -
457B LEU* 3.0 36.0 + - + +
460B VAL* 1.3 91.0 - - + +
462B LEU* 1.3 70.4 + - + +
498B ILE* 3.9 5.8 - - + +
499B ARG* 3.0 26.2 + - - +
----------------------------------------------------------
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