Contacts of the strand formed by residues 306 - 313 (chain A) in PDB entry 5H9U
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 ARG 306 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.3 18.0 - - - +
137A TYR* 3.2 22.5 + - - +
138A ALA 3.4 6.7 - - - +
139A THR* 3.4 24.5 - - - +
140A ASP* 5.3 0.7 - - - +
141A GLU* 4.9 7.5 + - - -
187A ASP* 4.8 20.4 - - - +
267A ALA 5.2 6.9 + - - -
268A VAL* 5.5 0.6 - - - +
304A ALA* 3.7 2.5 - - - +
305A ARG* 1.3 82.8 - - + +
307A ALA* 1.3 62.9 + - - +
326A GLU 4.4 0.7 - - - -
327A THR* 3.4 14.6 - - - -
328A PHE* 3.5 45.6 - - + -
330A THR* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 3.3 8.4 - - - -
138A ALA 2.9 35.4 + - - -
295A ALA* 3.6 12.5 - - - +
298A ILE* 4.0 25.6 - - + -
299A VAL* 3.7 17.4 - - + +
304A ALA* 4.4 2.9 - - + -
306A ARG* 1.3 75.3 - - - +
308A LEU* 1.3 60.3 + - - +
309A VAL* 5.3 0.2 - - + -
325A VAL* 5.0 3.6 - - + -
326A GLU 3.3 6.3 - - - +
327A THR* 4.6 3.1 - - + -
328A PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 4.0 31.4 - - + -
136A GLY 3.2 19.5 - - - +
137A TYR* 4.3 2.7 - - + -
268A VAL* 3.9 25.1 - - + -
269A PRO* 4.1 20.9 - - + -
307A ALA* 1.3 74.8 - - - +
309A VAL* 1.3 63.4 + - - +
310A GLU* 4.1 1.0 + - + +
324A ARG* 3.7 5.4 - - - +
325A VAL* 3.5 2.8 - - - +
326A GLU* 2.8 55.1 + - + +
328A PHE* 4.0 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A MET 3.8 0.3 - - - +
135A PHE* 3.4 4.7 - - - +
136A GLY 2.8 31.5 + - - +
291A ALA* 4.0 14.1 - - + +
294A MET* 3.6 38.1 - - + -
295A ALA* 3.7 30.7 - - + +
298A ILE* 4.3 13.5 - - + -
307A ALA* 5.1 0.7 - - + -
308A LEU* 1.3 79.0 - - - +
310A GLU* 1.3 64.0 + - - +
311A LEU 4.1 0.3 + - - -
323A LEU* 3.9 12.6 - - + -
324A ARG 3.3 8.3 - - - +
325A VAL* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.2 21.0 - - + +
134A MET 3.4 7.2 - - - +
135A PHE* 3.6 32.1 - - + -
308A LEU* 4.1 2.1 + - + -
309A VAL* 1.3 73.7 - - - +
311A LEU* 1.3 66.3 + - - +
312A ALA* 3.9 0.7 - - - +
322A SER* 3.3 33.7 + - - +
323A LEU* 3.3 8.1 - - - +
324A ARG* 2.9 66.7 + - + +
8C THR* 3.8 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.7 0.5 - - - -
134A MET* 2.8 44.9 + - + +
287A ALA* 3.4 28.9 - - + +
290A TYR* 4.7 2.7 - - + -
291A ALA* 4.3 5.6 - - + +
294A MET* 3.4 27.1 - - + -
309A VAL 4.1 0.4 + - - -
310A GLU* 1.3 77.7 - - - +
312A ALA* 1.3 62.0 + - - +
313A TYR* 3.6 21.5 - - + +
320A PRO* 4.5 4.7 - - + -
322A SER 3.5 3.8 - - - +
323A LEU* 3.5 30.7 - - + -
348A PRO* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 3.3 11.9 - - - +
133A LEU* 4.5 2.7 - - + -
310A GLU* 3.9 2.9 - - - +
311A LEU* 1.3 75.8 - - - +
313A TYR* 1.3 65.8 + - - +
320A PRO* 3.2 7.5 - - - +
321A VAL* 2.8 32.0 + - + -
322A SER* 3.0 29.7 + - - +
8C THR* 3.6 22.9 - - + -
179C GLN* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 3.8 17.5 - - + -
131A GLN* 3.4 2.8 - - - -
132A GLY 2.9 25.0 + - - +
134A MET* 3.4 22.2 - - + -
283A VAL* 4.4 13.7 - - + -
287A ALA* 3.4 22.2 - - + +
311A LEU* 3.6 23.7 - - + +
312A ALA* 1.3 77.2 - - - +
314A ALA* 1.3 60.0 + - - +
317A LYS 4.2 7.9 - - - -
318A ALA 3.8 16.4 - - - -
320A PRO* 3.8 21.5 - - + -
321A VAL* 4.3 2.0 - - - +
348A PRO* 2.4 42.4 + - - +
350A PRO* 4.5 6.7 - - + -
353A ILE* 3.7 8.2 - - + +
179C GLN* 2.8 19.3 + - - -
----------------------------------------------------------
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