Contacts of the strand formed by residues 160 - 164 (chain A) in PDB entry 3EUG
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 VAL 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 3.0 15.4 + - - +
58A VAL* 3.2 7.3 - - + +
59A VAL 2.8 25.3 + - - -
159A VAL* 1.3 73.7 - - - +
161A PHE* 1.3 63.3 + - - +
162A LEU* 3.5 27.8 - - + -
181A HIS* 3.3 12.3 - - + +
183A LEU* 4.3 8.1 - - + -
206A ALA* 3.8 33.0 - - + +
209A TRP* 3.3 34.3 - - + -
210A LEU* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.5 33.9 - - + -
61A LEU* 5.9 1.1 - - + -
149A ILE* 4.6 12.8 - - + -
152A ILE* 3.7 29.4 - - + -
153A ASN 4.8 5.6 - - - -
159A VAL* 3.6 27.4 - - + -
160A VAL* 1.3 74.6 - - - +
162A LEU* 1.3 63.1 + - - +
163A LEU* 3.8 13.0 + - + -
175A ILE* 3.6 54.3 - - + -
180A HIS* 3.9 11.7 - + + -
181A HIS 2.8 13.8 + - - +
182A VAL* 4.4 5.2 - - + +
183A LEU 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.9 25.1 - - + -
59A VAL 2.9 11.6 + - - +
60A ILE* 3.9 18.6 - - + +
61A LEU 3.8 20.1 + - - +
160A VAL* 3.5 22.9 - - + -
161A PHE* 1.3 72.6 - - - +
163A LEU* 1.3 66.8 + - - +
164A TRP* 3.7 34.9 + - + +
183A LEU* 3.6 21.1 - - + -
202A HIS* 3.9 27.8 - - + +
203A PHE* 4.8 2.5 - - + -
206A ALA* 4.7 1.6 - - + -
220A TRP* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL 5.5 0.4 - - - +
61A LEU* 3.9 22.0 - - + -
161A PHE* 4.2 16.8 - - + +
162A LEU* 1.3 77.7 - - - +
164A TRP* 1.3 61.6 + - - +
168A ALA* 3.8 25.4 - - - +
169A GLN* 3.3 26.5 + - + +
172A GLY* 3.8 26.0 - - - +
173A ALA* 5.5 0.4 - - - -
175A ILE* 4.5 3.6 - - + -
182A VAL* 3.7 29.2 - - + -
183A LEU 2.9 12.7 + - - +
184A LYS* 3.4 5.6 - - + -
185A ALA 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.5 31.4 - - + -
61A LEU 4.9 6.4 + - - +
77A PHE* 4.0 9.6 - + - -
92A MET* 3.7 32.8 - - + -
162A LEU* 3.7 21.8 + - + +
163A LEU* 1.3 80.0 - - - +
165A GLY* 1.3 61.9 + - - +
168A ALA* 3.3 18.9 + - - +
185A ALA* 3.1 12.6 - - + -
186A PRO 4.3 2.5 - - - -
187A HIS* 3.6 18.9 - - + -
188A PRO* 3.8 27.4 - - + -
197A PHE* 3.6 19.2 - + - -
202A HIS* 3.0 34.5 - + + -
203A PHE* 3.7 34.3 - + - -
----------------------------------------------------------
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