Contacts of the strand formed by residues 263 - 268 (chain C) in PDB entry 4HYY
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 ALA 263 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 4.5 0.4 - - + -
101C ILE* 4.0 15.3 - - + -
116C ILE* 4.0 24.0 - - + +
117C GLU 4.0 2.5 - - - +
118C SER* 3.5 25.8 - - - +
218C LYS 2.9 14.6 + - - +
219C LEU* 3.3 5.0 - - + +
220C LEU* 2.8 26.9 + - - +
262C VAL* 1.3 74.4 - - - +
264C VAL* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.7 3.2 - - - +
120C ALA 3.1 15.0 + - - +
121C ILE* 3.3 29.4 - - + -
122C THR* 2.7 34.1 + - - -
220C LEU* 3.3 20.4 - - + +
222C ILE* 5.2 0.7 - - + -
253C LEU* 4.2 23.8 - - + +
256C ILE* 5.5 0.2 - - + -
257C SER* 3.9 28.3 - - - +
262C VAL* 4.5 3.1 - - + +
263C ALA* 1.3 75.6 - - - +
265C PHE* 1.3 54.9 + - - +
266C VAL* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.0 28.0 - - + -
122C THR* 3.3 14.4 - - + -
124C ALA* 3.8 27.6 - - + -
132C LYS 4.5 0.2 - - - -
135C LEU* 3.6 31.0 - - + -
136C SER* 3.6 24.2 - - - -
139C LEU* 3.6 21.8 - - + -
219C LEU* 4.0 17.7 - - + +
220C LEU 3.0 6.7 + - - -
221C ILE* 3.5 14.5 - - + +
222C ILE 3.1 22.0 + - - -
264C VAL* 1.3 72.6 - - - +
266C VAL* 1.3 66.6 + - - +
267C THR* 3.7 17.0 - - + -
301C ILE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.5 11.2 - - + -
122C THR 2.7 12.5 + - - +
123C GLU* 3.1 27.0 - - + -
124C ALA* 2.8 31.4 + - - +
222C ILE* 3.3 20.9 - - + +
225C ILE* 3.8 42.6 - - + -
250C LEU* 6.3 0.2 - - + -
253C LEU* 4.6 0.7 - - + -
264C VAL* 3.9 20.2 - - + -
265C PHE* 1.3 82.8 - - - +
267C THR* 1.3 59.9 + - - +
293C LEU* 5.3 2.5 - - + -
297C SER* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA 3.1 7.2 - - - +
132C LYS* 3.7 38.5 - - + +
136C SER* 3.8 7.4 - - - +
221C ILE* 6.0 0.2 - - + -
222C ILE 3.3 4.2 + - - +
223C ASP* 2.5 28.5 + - - +
224C SER* 3.1 11.8 - - - -
225C ILE* 2.9 31.4 + - - +
265C PHE* 3.7 27.8 - - + -
266C VAL* 1.3 74.0 - - - +
268C ASN* 1.3 62.3 + - - +
269C GLN* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLU* 3.2 31.3 - - + +
124C ALA 3.0 4.8 + - - -
125C PHE* 3.2 22.8 - - + -
126C GLY 3.5 1.0 + - - -
132C LYS* 3.3 15.0 + - - -
224C SER* 4.4 0.6 - - - -
225C ILE* 3.8 15.5 - - + +
226C MET* 4.1 6.3 - - - +
267C THR* 1.3 76.0 - - - +
269C GLN* 1.3 92.0 + - - +
287C PRO* 3.9 4.2 - - - +
288C ILE* 3.1 37.3 + - - +
293C LEU* 3.3 9.5 - - - +
----------------------------------------------------------
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