Contacts of the strand formed by residues 210 - 214 (chain A) in PDB entry 5KCJ
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 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.8 14.8 - - + -
138A MET 3.3 6.3 - - - -
139A VAL* 3.8 13.2 - - + -
153A PHE* 3.9 3.6 - - + -
163A PHE* 3.7 22.2 - - + -
164A ARG 3.1 4.4 + - - -
165A PHE* 3.2 31.2 - - + -
166A GLY 3.3 4.7 + - - -
203A LEU* 3.9 5.2 - - - -
208A LEU* 3.4 6.8 - - - +
209A ASP* 1.3 79.3 - - - +
211A PHE* 1.3 60.7 + - - +
212A ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.4 1.6 - - - -
138A MET* 2.7 38.8 + - + +
166A GLY 3.4 14.6 - - - -
167A THR* 4.0 8.1 - - - -
168A VAL* 3.9 21.5 - - + -
193A GLN* 4.6 3.1 - - + -
196A VAL* 4.2 18.8 - - + -
199A ALA* 3.5 32.3 - - + -
200A LEU* 4.6 10.1 - - + -
203A LEU* 3.7 18.2 - - + -
208A LEU* 4.2 6.5 - - + -
210A ALA* 1.3 74.5 - - - +
212A ILE* 1.3 69.4 + - - +
213A TYR* 3.6 22.4 - + + -
218A LEU* 3.7 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.4 30.7 - - + -
136A SER 3.5 5.4 - - - +
137A VAL* 4.1 17.0 - - + -
148A LEU* 4.1 18.4 - - + -
153A PHE* 4.1 12.6 - - + -
165A PHE* 3.6 33.2 - - + -
166A GLY 2.9 10.5 + - - +
167A THR* 2.7 33.0 + - - -
173A THR* 4.0 1.6 - - + -
177A ILE* 3.9 17.9 - - + -
184A MET* 4.6 1.8 - - - -
188A MET* 3.8 15.9 - - + -
211A PHE* 1.3 73.6 - - - +
213A TYR* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 2.6 28.0 + - - -
86A LYS* 5.2 4.7 + - - -
87A HIS* 4.5 4.3 - - - -
134A GLY 4.5 0.2 - - - -
135A ILE* 3.8 0.6 - - - -
136A SER 2.9 30.1 + - - +
167A THR* 4.1 9.2 - - - -
168A VAL* 3.7 28.5 - - + +
173A THR* 3.8 12.3 - - - -
196A VAL* 3.4 26.3 - - + +
211A PHE* 3.6 22.9 - + + -
212A ILE* 1.3 75.4 - - - +
214A ASP* 1.3 91.3 + - + +
217A VAL* 3.8 11.9 - - + -
218A LEU* 3.5 16.1 - - + +
302A GLU* 3.5 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 5.9 0.2 - - - -
115A THR* 3.7 7.4 + - - -
133A THR* 2.7 23.6 + - - +
134A GLY 3.5 7.9 - - - +
173A THR* 3.6 0.4 + - - -
213A TYR* 1.3 92.4 - - + +
215A ALA* 1.3 63.4 + - - +
216A ALA 3.2 2.6 + - - -
217A VAL* 2.8 23.6 + - + +
218A LEU* 3.1 21.5 + - - +
244A TYR* 2.7 37.7 + - - -
302A GLU* 3.1 27.8 + - + +
----------------------------------------------------------
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