Contacts of the strand formed by residues 115 - 119 (chain B) in PDB entry 5YGP
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 SER 115 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA 4.0 2.4 + - - -
114B LEU* 1.3 79.6 + - - +
116B LEU* 1.3 62.1 + - - +
117B ILE* 3.6 4.6 + - - +
227B ILE* 3.6 5.0 - - - -
228B ASN 3.2 28.2 + - - +
233B TRP* 5.8 1.3 - - - -
245B VAL* 3.6 25.7 - - - +
246B THR 3.6 1.8 - - - -
248B LEU* 3.5 8.5 - - - -
320B ALA 3.4 9.9 + - - -
321B THR* 3.8 11.9 + - - -
324B ASN* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 1.3 71.8 - - - +
117B ILE* 1.3 63.0 + - - +
118B TYR* 4.1 1.5 + - + -
126B PRO* 4.1 19.3 - - + -
127B PRO 4.1 6.1 - - - +
130B TRP* 6.5 0.2 - - + -
133B ILE* 6.0 0.9 - - + -
148B LEU* 4.8 3.8 - - + -
225B MET* 4.0 30.7 - - + -
226B THR 3.8 11.2 - - - +
227B ILE* 4.4 12.6 - - + -
244B GLY 3.6 1.2 - - - +
245B VAL* 3.4 3.8 - - - -
246B THR* 2.9 50.9 + - + +
247B VAL 3.6 19.1 - - - +
248B LEU* 3.4 9.7 - - + +
249B PRO* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER 3.9 6.7 - - - +
116B LEU* 1.3 77.2 - - - +
118B TYR* 1.3 60.4 + - - +
218B PHE* 3.5 20.9 - - + -
225B MET* 3.2 3.0 - - - +
226B THR* 2.7 47.5 + - + +
228B ASN* 4.0 33.7 - - + +
229B GLY 4.5 0.2 - - - +
232B ALA* 5.3 0.2 - - + -
233B TRP* 3.8 26.5 - - + +
236B ILE* 4.1 11.0 - - + -
243B TYR* 3.5 31.2 - - + -
244B GLY 3.2 4.3 - - - +
245B VAL* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.4 1.3 - - + -
117B ILE* 1.3 75.6 - - - +
119B ASN* 1.3 59.3 + - - +
120B LYS* 3.9 24.5 - - + +
123B LEU* 3.1 30.5 - - + -
124B PRO 4.2 6.2 + - - -
126B PRO* 3.6 40.3 - - + +
218B PHE* 3.7 5.2 - - - -
224B ALA 3.2 10.5 - - - +
225B MET* 3.9 15.3 - - + -
243B TYR* 3.1 3.3 - - - +
244B GLY* 2.6 68.7 + - - -
245B VAL 4.1 1.3 - - - -
246B THR* 4.0 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 1.3 73.4 - - - +
120B LYS* 1.3 55.7 + - - +
121B ASP* 2.6 40.2 + - - +
122B LEU* 3.4 37.3 - - + +
123B LEU* 2.8 35.9 + - - +
218B PHE* 3.7 14.1 - - + +
221B GLY* 4.7 10.5 - - - -
223B THR 4.9 1.1 - - - +
224B ALA 2.9 14.9 + - - +
241B VAL* 5.5 8.6 - - + +
242B ASN 2.8 17.0 - - - +
243B TYR* 4.1 1.1 - - + +
----------------------------------------------------------
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