Contacts of the strand formed by residues 279 - 286 (chain A) in PDB entry 2Y60
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 ARG 279 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 3.9 5.7 - - - +
189A TYR* 2.8 76.4 + - + +
210A SER* 4.9 1.0 + - - -
225A GLN* 4.0 13.1 - - - +
226A SER* 3.6 19.3 - - - +
228A VAL* 4.1 32.1 - - + -
230A ASN* 3.5 32.9 + - - +
272A VAL* 3.5 27.3 - - - +
273A LYS 4.2 4.2 + - - -
275A VAL* 4.6 11.7 + - - +
277A ALA* 3.7 11.3 + - - +
278A GLU* 1.3 77.3 - - - +
280A GLN* 1.3 73.2 + - - +
281A SER* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.0 49.0 + - - -
58A THR* 3.8 12.8 - - + +
59A LYS* 3.3 24.5 - - - +
62A HIS* 4.8 5.5 + - - +
187A ILE 3.5 6.1 - - - +
189A TYR* 5.3 0.2 - - - -
224A TYR* 3.8 9.3 + - + -
225A GLN* 3.4 7.3 - - - +
226A SER* 2.8 36.1 + - - +
279A ARG* 1.3 87.2 + - - +
281A SER* 1.3 60.8 + - - +
282A LEU* 4.0 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 2.9 44.8 + - - +
189A TYR* 4.1 13.4 - - - -
223A LEU* 3.6 3.1 - - - +
224A TYR 3.8 3.1 - - - -
225A GLN* 2.9 20.3 + - - +
279A ARG* 4.5 0.9 - - - -
280A GLN* 1.3 75.5 - - - +
282A LEU* 1.3 57.9 + - - +
283A PRO* 3.3 2.9 - - - +
1332A M8F 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.6 30.1 - - + +
55A SER* 4.8 0.2 - - - -
58A THR* 3.9 28.5 - - + +
145A TYR* 4.7 10.1 + - + +
184A VAL* 5.7 1.1 - - + -
185A VAL 3.3 5.4 - - - +
186A LEU* 3.7 27.6 - - + -
187A ILE 3.7 3.8 - - - +
222A VAL 4.0 1.4 - - - +
223A LEU* 3.7 2.8 - - - +
224A TYR* 2.8 61.7 + - + +
280A GLN* 4.0 12.3 - - + +
281A SER* 1.3 89.3 + - - +
283A PRO* 1.3 66.8 - - - +
284A PHE 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 6.3 0.7 - - - -
183A SER 3.8 0.9 - - - +
184A VAL* 3.4 5.5 - - - +
185A VAL* 3.0 45.5 + - + +
187A ILE* 3.9 6.5 - - + -
221A THR* 4.4 5.8 - - + -
222A VAL 3.9 2.7 - - - +
223A LEU* 3.5 19.0 - - + -
281A SER* 3.3 8.7 - - - +
282A LEU* 1.3 91.3 - - - +
284A PHE* 1.3 60.0 + - - +
285A PHE* 3.6 30.5 - - + -
1332A M8F 3.8 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 5.3 2.9 - - + +
146A TYR* 3.9 23.1 - + - -
149A VAL* 3.5 39.3 - - + -
150A PHE* 4.0 19.5 - + + -
153A SER* 3.2 34.5 - - - -
175A PHE* 4.0 7.0 - + - -
182A ALA* 3.5 28.7 - - + -
183A SER 3.3 12.6 - - - -
184A VAL* 3.6 10.5 - - + -
221A THR* 3.7 1.4 - - - -
222A VAL* 2.9 42.7 + - + +
283A PRO* 1.3 71.7 - - - +
285A PHE* 1.3 63.9 + - - +
286A VAL* 3.5 12.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.1 23.5 - - - +
183A SER* 2.9 33.1 + - - +
185A VAL* 3.9 8.1 - - + -
216A ASP* 4.4 2.7 - - + -
217A VAL 4.2 16.2 - - - +
218A SER* 4.3 0.7 - - - -
220A ILE 4.1 2.0 - - - -
221A THR* 3.6 33.9 - - + -
283A PRO* 3.6 22.9 - - + -
284A PHE* 1.3 70.9 - - - +
286A VAL* 1.3 62.2 + - - +
287A ASN* 3.1 22.9 + - - +
1332A M8F 3.3 75.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 3.3 28.7 - - - +
157A LEU* 4.0 26.0 - - + -
175A PHE* 3.7 21.8 - - + -
182A ALA* 4.4 4.0 - - - -
218A SER* 4.3 0.6 - - - -
219A LEU* 2.9 36.7 + - + +
220A ILE* 2.9 42.3 + - + +
222A VAL* 3.7 9.0 - - + -
284A PHE* 3.8 8.3 - - + +
285A PHE* 1.3 66.6 - - - +
287A ASN* 1.3 59.5 + - - +
288A LEU* 5.2 0.2 - - + -
----------------------------------------------------------
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