Contacts of the strand formed by residues 214 - 224 (chain A) in PDB entry 1QQW
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 GLY 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 4.0 2.9 - - - -
148A ASN 3.2 10.5 - - - -
213A ASN* 1.3 77.0 - - - +
215A TYR* 1.3 68.9 + - - -
236A TYR* 2.8 60.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY* 3.2 3.5 - - - -
148A ASN 3.1 25.6 + - - -
149A ASN 3.0 24.9 - - - -
150A THR 3.3 22.2 - - - +
151A PRO* 3.3 31.5 - - + +
203A ARG* 3.2 29.3 + - - -
213A ASN* 3.4 24.7 + - + +
214A GLY* 1.3 84.5 - - - -
216A GLY* 1.3 62.2 - - - +
217A SER* 2.9 11.1 + - - +
234A PHE 3.0 10.3 - - - +
235A HIS* 3.2 32.8 - - + +
236A TYR* 3.6 7.5 - - - -
237A LYS* 5.1 8.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.4 17.5 - - - -
146A VAL 4.3 2.2 - - - +
147A GLY* 4.5 5.6 - - - -
215A TYR* 1.3 70.1 - - - +
217A SER* 1.3 58.6 + - - +
218A HIS* 2.6 33.6 + - - +
220A PHE* 4.2 8.0 - - - -
234A PHE* 2.8 28.5 + - - +
236A TYR* 4.2 0.8 - - - -
600A HEM 3.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 4.2 2.9 + - - +
150A THR 2.8 26.9 + - - -
151A PRO* 3.7 21.4 - - - +
152A ILE* 4.1 3.3 + - - -
215A TYR* 2.9 11.1 + - - +
216A GLY* 1.3 79.6 - - - +
218A HIS* 1.3 65.0 + - - +
233A LYS* 3.4 21.7 + - - +
234A PHE 4.5 1.8 + - - +
299A LEU* 3.8 19.9 - - - +
600A HEM 3.9 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY* 2.6 19.4 + - - +
217A SER* 1.3 79.1 + - - +
219A THR* 1.3 64.8 + - - +
220A PHE* 3.7 25.0 - + + -
232A CYS 4.0 1.6 - - - +
233A LYS* 3.4 11.9 - - - +
299A LEU* 3.5 31.6 - - + +
348A ASP* 2.8 25.4 + - - +
350A MET* 3.6 16.2 - - + -
351A LEU* 3.8 27.3 - - + +
354A ARG* 2.9 41.8 + - - -
600A HEM 4.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 1.3 72.8 - - - +
220A PHE* 1.3 72.3 + - - +
231A TYR* 3.9 21.1 - - + -
232A CYS 3.5 7.2 - - - +
233A LYS* 3.2 21.5 + - - +
296A PRO 2.9 22.6 + - - -
297A PHE* 3.8 25.7 - - + -
303A TRP* 3.5 8.0 - - + -
346A SER* 3.1 23.5 + - - +
348A ASP* 4.1 4.6 + - - +
351A LEU* 4.0 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 6.1 2.0 - - - -
144A ASP 6.2 0.2 - - - -
145A LEU* 4.6 11.4 - - + -
146A VAL 5.9 1.8 - - - -
216A GLY* 4.2 13.5 - - - -
218A HIS* 3.7 30.7 - + + -
219A THR* 1.3 76.1 - - - +
221A LYS* 1.3 62.6 + - - +
231A TYR* 3.2 11.7 - - - -
232A CYS* 2.8 46.2 + - - -
234A PHE* 3.8 30.5 - + + -
336A PRO* 5.1 4.7 - - + -
339A MET* 4.0 20.9 - - + -
343A ILE* 4.7 5.8 - - + -
344A GLU 3.8 14.1 - - - +
346A SER* 4.5 2.7 - - - -
351A LEU* 3.9 31.4 - - + -
354A ARG* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 1.3 76.6 - - - +
222A LEU* 1.3 69.9 + - - +
223A VAL* 4.6 0.4 - - - -
229A ALA* 4.0 16.2 - - + -
230A VAL 3.6 5.4 - - - +
231A TYR* 4.3 15.7 - - + -
286A PHE* 4.7 1.6 - - + -
343A ILE* 3.5 5.7 - - - +
344A GLU* 2.9 69.9 + - - +
345A ALA 3.3 18.6 + - - +
346A SER* 5.9 0.2 - - - -
421A HIS* 3.1 41.8 + - + +
423A ILE* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 5.6 4.9 - - + -
94A TYR* 3.9 31.0 - - + +
95A SER* 3.7 13.2 - - - -
100A PHE* 5.1 3.1 - - + -
221A LYS* 1.3 78.8 - - - +
223A VAL* 1.3 63.8 + - - +
228A GLU 3.6 0.9 - - - +
229A ALA* 2.9 26.5 - - - +
230A VAL* 2.7 26.9 + - + +
232A CYS* 3.4 34.8 - - + -
234A PHE* 4.7 9.0 - - + -
281A ILE* 5.1 12.6 - - + -
283A VAL* 5.5 1.1 - - + -
342A GLY 3.5 14.1 - - - +
343A ILE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR 3.3 3.8 - - - -
95A SER* 3.4 0.7 - - - -
96A LYS* 2.9 27.6 + - + +
221A LYS* 4.6 3.8 - - + -
222A LEU* 1.3 80.6 - - - +
224A ASN* 1.3 72.9 + - - +
227A GLY* 3.8 21.3 - - - +
228A GLU 3.3 9.0 - - - +
229A ALA* 4.0 6.5 - - + -
342A GLY* 3.0 23.1 + - - +
344A GLU* 4.0 19.7 - - + +
421A HIS* 3.8 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR 4.0 8.1 - - - +
93A LYS* 3.8 21.9 + - - +
94A TYR 3.1 16.4 + - - +
95A SER 4.1 0.2 - - - -
96A LYS* 3.6 17.1 + - - +
223A VAL* 1.3 79.3 - - - +
225A ALA* 1.3 61.1 + - - +
226A ASN* 2.8 25.0 + - - +
227A GLY* 3.1 8.3 + - - -
228A GLU* 2.8 53.7 + - - +
----------------------------------------------------------
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