Contacts of the strand formed by residues 212 - 220 (chain A) in PDB entry 4Z1H
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 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.1 18.5 + - - +
209A PHE* 3.7 10.9 - - + +
211A VAL* 1.3 81.1 - - - +
213A ASP* 1.3 60.8 + - - +
214A ARG 4.0 1.3 - - - +
215A VAL* 3.8 22.2 - - + -
234A ASP 5.5 0.7 - - - +
255A ILE* 3.6 17.5 - - + -
256A HIS 3.2 13.0 - - - +
257A LEU* 4.3 0.2 - - - +
258A LYS* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 6.0 0.7 - - - -
212A ALA* 1.3 75.0 - - - +
214A ARG* 1.3 72.7 + - - +
234A ASP* 3.7 27.7 - - - +
256A HIS* 2.8 31.8 + - - +
257A LEU 4.1 10.6 - - - +
258A LYS* 3.9 16.0 - - + +
259A SER 5.6 0.3 + - - -
262A LYS* 5.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 5.7 0.4 - - - -
212A ALA* 3.5 1.2 - - - +
213A ASP* 1.3 92.6 + - - +
215A VAL* 1.3 70.5 - - - +
216A GLU* 5.0 4.9 + - - -
232A LEU* 6.1 6.3 - - + -
233A SER 3.5 15.7 - - - +
234A ASP* 4.4 4.7 - - + +
256A HIS* 2.9 73.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 4.0 18.4 - - + -
208A ALA* 4.3 12.8 - - + -
209A PHE* 3.6 30.5 - - + -
212A ALA* 3.8 17.7 - - + -
214A ARG* 1.3 81.4 - - - +
216A GLU* 1.3 62.5 + - - +
217A VAL* 3.7 22.9 - - + -
231A TRP* 3.7 5.0 - - + +
232A LEU* 3.4 5.9 - - - +
233A SER 2.9 34.9 + - - +
253A ILE* 4.4 7.0 - - + -
254A ILE 3.6 6.5 - - - +
255A ILE* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ARG* 5.0 4.7 + - - -
215A VAL* 1.3 73.7 - - - +
217A VAL* 1.3 57.9 + - - +
218A TYR* 2.3 46.7 + - + +
230A GLN* 4.6 1.0 + - - -
231A TRP 3.7 4.0 - - - -
232A LEU* 3.8 17.5 - - + -
252A LYS 3.9 0.5 - - - +
254A ILE* 2.7 59.8 + - + +
256A HIS* 3.1 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 4.8 2.5 - - + -
168A LEU* 5.1 0.9 - - + -
205A PHE* 4.0 13.2 - - + -
215A VAL* 3.7 22.0 - - + -
216A GLU* 1.3 78.6 - - - +
218A TYR* 1.3 69.2 + - - +
219A SER* 4.7 5.2 - - - -
229A TYR 3.6 1.0 - - - +
230A GLN* 3.4 3.8 - - - +
231A TRP* 2.8 57.0 + - + +
251A THR* 3.9 21.5 - - + -
252A LYS 3.2 8.7 - - - +
253A ILE* 3.9 18.4 - - + -
601A 4KP 4.4 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.6 42.0 - - + +
81A VAL* 4.8 2.2 - - + -
216A GLU* 2.3 48.5 + - + -
217A VAL* 1.3 73.4 - - - +
219A SER* 1.3 61.2 + - - +
229A TYR 3.3 3.6 - - - -
230A GLN* 3.3 45.4 + - + -
244A ALA* 4.3 5.6 - - + -
247A VAL* 3.9 23.7 - - + +
250A GLY 4.1 0.7 - - - +
251A THR* 3.6 0.7 - - - +
252A LYS* 2.7 59.1 + - + +
254A ILE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY 3.9 0.2 - - - -
163A MET* 3.2 44.6 + - - +
168A LEU* 4.4 13.2 - - - +
217A VAL* 4.7 2.5 - - - -
218A TYR* 1.3 76.5 - - - +
220A ARG* 1.3 60.9 + - - +
221A SER 4.3 0.2 - - - -
227A LEU 4.1 1.4 - - - +
228A GLY* 3.4 0.3 - - - -
229A TYR* 2.9 34.2 + - - +
247A VAL* 3.6 4.4 - - - +
250A GLY 3.5 5.5 + - - -
251A THR* 3.1 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY* 3.4 6.6 - - - -
219A SER* 1.3 76.3 + - - +
221A SER* 1.3 73.8 + - - +
226A SER* 3.4 29.4 + - - +
227A LEU 4.1 2.5 - - - -
228A GLY* 3.8 17.5 - - - +
247A VAL* 2.8 45.2 + - + +
248A ARG* 3.7 9.0 - - - +
249A THR* 3.5 28.6 + - - +
250A GLY 3.0 29.5 + - - -
----------------------------------------------------------
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