Contacts of the strand formed by residues 184 - 189 (chain I) in PDB entry 3SDI
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 184 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H ILE* 3.7 5.6 - - - +
219H VAL* 2.8 48.3 + - + +
221H ILE* 3.5 31.1 - - + +
42I PHE* 3.7 25.4 - - + -
176I TYR* 4.0 10.5 - - + -
177I ILE 3.3 8.7 - - - +
178I ILE* 3.8 28.0 - - + -
179I LYS 4.5 2.7 - - - +
183I GLU* 1.3 82.1 - - - +
185I VAL* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H GLU* 4.0 26.5 - - + +
217H SER 3.8 10.8 - - - +
218H ILE* 4.7 7.6 - - + +
175I VAL 3.6 0.9 - - - +
176I TYR* 3.3 5.5 - - - +
177I ILE* 2.8 42.8 + - + +
179I LYS* 6.1 2.2 - - + -
183I GLU* 3.9 24.9 - - + +
184I VAL* 1.3 78.0 - - - +
186I LYS* 1.3 63.2 + - - +
187I ARG* 4.1 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LYS 4.0 0.2 - - - +
216H GLU* 3.4 5.2 - - - +
217H SER* 2.9 44.9 + - - +
219H VAL* 3.7 15.5 - - + -
32I GLU* 3.3 15.4 + - - -
174I VAL* 3.6 18.6 - - + -
175I VAL 3.4 2.9 - - - +
176I TYR* 3.1 39.9 + - + +
185I VAL* 1.3 75.7 - - - +
187I ARG* 1.3 65.1 + - - +
188I TYR* 3.0 36.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H VAL* 4.0 20.5 - - + +
215H LYS 3.5 3.4 - - - +
216H GLU* 3.8 32.6 + - + -
148I PRO 5.5 0.8 + - - -
149I GLU* 5.8 8.3 - - - +
152I PHE* 3.6 46.8 - - + +
174I VAL* 3.4 4.0 - - - -
175I VAL* 2.8 42.3 + - - +
177I ILE* 3.7 27.3 - - - +
185I VAL* 4.1 20.8 - - - +
186I LYS* 1.3 78.9 - - - +
188I TYR* 1.3 66.0 + - - +
189I LEU* 3.8 1.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H VAL* 3.6 4.0 - - - +
214H LEU* 2.6 43.3 + - + -
215H LYS* 3.0 50.0 + - + +
216H GLU* 5.7 0.4 - - - -
217H SER* 5.7 2.7 - - - -
18I LEU* 4.2 18.8 - - + -
32I GLU* 2.8 27.6 + - - -
173I ALA 3.4 5.4 - - - +
174I VAL* 3.8 20.0 - - + -
186I LYS* 3.0 28.0 + - + -
187I ARG* 1.3 75.3 - - - +
189I LEU* 1.3 58.6 + - - +
210Y ILE* 4.0 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H THR* 3.8 15.9 - - + -
212H ALA 3.6 6.1 - - - +
213H VAL* 4.8 1.8 - - + -
214H LEU* 3.3 14.3 - - - +
152I PHE* 3.8 16.2 - - + -
156I SER* 3.6 28.9 - - - +
159I LEU* 4.0 6.1 - - + -
160I LEU* 3.8 21.3 - - + -
172I GLY* 4.8 3.6 - - - -
173I ALA* 3.0 45.0 + - + +
175I VAL* 3.8 25.1 - - + -
187I ARG* 4.5 2.5 - - + +
188I TYR* 1.3 76.8 - - - +
190I LYS* 1.3 67.1 + - - +
191I MET* 3.8 1.8 + - + +
210Y ILE* 5.8 0.3 - - - +
----------------------------------------------------------
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