Contacts of the helix formed by residues 515 - 527 (chain A) in PDB entry 1YI1
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 PHE 515 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.7 28.9 - + + -
152A GLU* 3.8 19.7 - - + -
153A GLY 5.0 0.2 - - - -
156A ARG* 3.5 29.4 - - - -
181A ASP* 3.6 21.1 - - - -
483A THR 3.4 17.5 + - - +
484A GLY* 5.0 1.2 - - - -
505A LEU 3.8 15.7 - - - -
506A SER* 3.8 2.0 - - - -
507A SER* 3.8 23.8 - - - -
512A ALA 3.4 20.8 + - - +
513A MET 3.2 0.2 - - - -
514A GLY* 1.3 79.1 - - - +
516A GLY* 1.3 60.2 + - - +
517A LEU 3.7 0.2 - - - -
518A PRO* 3.4 2.5 - - - +
519A ALA* 2.9 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 2.5 28.7 + - - -
483A THR 3.2 22.0 + - - -
484A GLY* 4.3 2.0 - - - -
514A GLY* 3.6 0.8 - - - -
515A PHE* 1.3 73.0 - - - +
517A LEU* 1.3 66.5 + - - +
520A ALA* 2.9 12.5 + - - +
534A ASP* 3.5 15.9 - - - -
536A ASP* 4.0 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLY 5.0 0.8 + - - -
516A GLY* 1.3 73.5 - - - +
518A PRO* 1.3 72.0 - - + +
520A ALA* 3.3 4.4 + - - +
521A ILE* 3.2 21.9 + - - +
534A ASP* 3.3 19.5 + - - +
536A ASP* 3.5 6.5 + - - +
541A PHE* 3.8 17.5 - - + +
544A ASN* 3.7 22.2 - - + +
545A VAL* 4.3 2.5 - - - +
547A GLU* 4.2 3.8 - - + -
548A LEU* 3.5 37.5 - - + +
551A ILE* 3.4 26.2 - - + -
558A VAL* 4.7 3.1 - - + -
560A VAL* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 3.8 18.2 - - - +
149A PHE* 3.5 20.4 - - + -
150A ALA* 3.3 9.8 - - - -
514A GLY 3.5 21.1 - - - +
515A PHE 3.4 8.3 - - - +
517A LEU* 1.3 93.2 - - + +
519A ALA* 1.3 64.2 + - - +
521A ILE* 3.0 29.2 + - + +
522A GLY 3.2 5.0 + - - -
544A ASN* 3.9 20.0 - - + +
547A GLU* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE 3.5 14.3 + - - +
153A GLY* 3.5 14.1 - - - -
482A SER* 3.5 14.1 - - - +
505A LEU* 4.8 3.4 - - + -
515A PHE* 2.9 50.2 + - + +
518A PRO* 1.3 77.0 - - - +
520A ALA* 1.3 63.3 + - - +
522A GLY 3.1 2.3 + - - -
523A ALA* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 3.5 16.6 + - - -
516A GLY 2.9 13.5 + - - +
517A LEU 3.3 11.9 - - - +
519A ALA* 1.3 77.2 - - - +
521A ILE* 1.3 61.4 + - - +
523A ALA* 3.3 2.1 + - - -
524A SER* 2.9 26.9 + - - -
532A VAL* 3.6 14.1 - - + +
534A ASP* 4.0 8.3 - - + -
558A VAL* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 4.5 7.6 - - + -
139A VAL* 4.4 12.3 - - + -
146A GLY 6.0 0.2 - - - +
150A ALA* 4.7 4.5 - - + -
517A LEU 3.3 13.9 - - - +
518A PRO* 3.0 12.1 + - + +
520A ALA* 1.3 77.2 - - - +
522A GLY* 1.3 62.1 + - - +
524A SER* 3.4 2.3 + - - -
525A VAL* 3.1 24.2 + - + +
547A GLU* 3.7 42.0 - - + +
550A THR* 3.7 24.7 - - + -
551A ILE* 3.6 19.5 - - + -
556A LEU* 3.6 22.2 - - + +
558A VAL* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 4.1 13.9 - - - -
150A ALA* 3.3 25.0 + - - +
154A TYR* 3.7 12.5 - - - -
518A PRO 3.2 4.6 + - - -
519A ALA 3.1 5.7 + - - -
521A ILE* 1.3 77.1 - - - +
523A ALA* 1.3 63.8 + - - +
525A VAL 3.3 1.4 + - - -
526A ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLY 3.8 2.4 - - - -
157A SER* 3.2 19.5 - - - -
480A ILE* 3.9 13.2 - - + -
505A LEU* 3.3 32.3 - - + -
519A ALA 2.9 10.1 + - - +
520A ALA* 3.7 4.7 - - - +
522A GLY* 1.3 75.0 - - - +
524A SER* 1.3 57.8 + - - +
527A ASN* 2.7 36.8 + - - +
532A VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ALA 2.9 17.1 + - - -
521A ILE 3.6 4.5 - - - -
523A ALA* 1.3 75.4 - - - +
525A VAL* 1.3 61.3 + - - +
527A ASN 3.0 27.2 + - - +
528A PRO* 3.0 7.1 - - - +
532A VAL* 3.9 17.9 - - - +
556A LEU* 3.9 9.8 - - - +
557A PRO* 3.6 31.5 - - - +
558A VAL* 4.0 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.8 33.0 + - + +
116A PHE* 4.7 5.6 - - + -
137A ARG* 4.0 24.7 - - - +
139A VAL* 4.2 14.6 - - + -
154A TYR* 4.4 2.6 - - + -
521A ILE* 3.1 19.5 + - + +
522A GLY 3.3 4.9 + - - +
524A SER* 1.3 76.1 - - - +
526A ALA* 1.3 59.7 + - - +
527A ASN 3.7 0.3 + - - -
528A PRO* 3.8 13.4 - - - +
554A GLU* 5.9 0.2 - - + -
556A LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.8 29.8 - - + +
157A SER* 3.5 19.7 - - - +
158A SER* 4.4 11.6 - - - -
160A LYS* 5.9 3.0 + - - +
522A GLY 3.0 17.2 + - - +
524A SER 3.1 0.2 - - - -
525A VAL* 1.3 76.1 - - - +
527A ASN* 1.3 66.8 + - - +
528A PRO* 3.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 3.0 40.0 + - - +
158A SER* 5.4 0.9 - - - -
480A ILE* 3.5 13.3 - - + +
523A ALA 2.7 24.4 + - - +
524A SER* 3.0 11.9 + - - +
526A ALA* 1.3 86.0 - - - +
528A PRO* 1.3 66.4 - - - +
529A ASP 3.3 2.9 - - - -
530A ALA* 3.1 33.5 + - + +
532A VAL* 4.5 0.5 - - - +
----------------------------------------------------------
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