Contacts of the strand formed by residues 355 - 366 (chain A) in PDB entry 1C5G
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 355 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLY 3.3 11.7 - - - -
197A GLN* 4.1 0.7 - - - -
198A TRP* 3.1 21.1 + - - -
350A GLU 3.9 0.4 - - - +
351A VAL* 3.7 0.5 - - - -
352A ASN* 2.9 38.2 + - - +
354A SER* 1.3 80.6 - - - +
356A THR* 1.3 65.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 3.7 14.3 - - + +
195A ASN* 3.6 2.3 + - - -
196A GLY 2.8 33.4 + - - +
198A TRP* 3.7 4.7 - - - -
251A TYR* 3.0 31.3 + - - +
258A MET* 3.4 12.9 - - + +
349A ILE* 3.9 28.3 - - + -
350A GLU 3.3 9.4 - - - +
351A VAL* 3.7 6.6 - - + +
355A GLY* 1.3 77.0 + - - -
357A VAL* 1.3 67.3 + - - +
358A ALA* 4.4 0.9 - - + +
385A VAL* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 4.0 20.3 - - + +
193A TYR* 4.2 14.6 - - + +
194A PHE 3.2 7.9 - - - +
195A ASN* 3.4 24.5 - - - +
349A ILE* 3.4 1.6 - - - +
350A GLU* 2.7 69.1 + - + +
356A THR* 1.3 76.6 - - - +
358A ALA* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 4.1 2.7 - - - -
193A TYR* 3.7 4.5 - - - -
194A PHE* 2.8 32.6 + - + +
348A LYS 3.3 8.5 - - - +
349A ILE* 3.7 26.7 - - + -
356A THR* 4.2 4.9 - - + +
357A VAL* 1.3 74.5 - - - +
359A SER* 1.3 65.2 + - - +
395A PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 3.2 26.7 + - - -
170A MET* 3.6 26.0 - - - +
171A ILE* 3.8 13.9 - - - -
192A LEU 3.1 11.9 + - - -
193A TYR* 3.8 4.9 - - - -
347A VAL* 3.2 9.4 - - - +
348A LYS* 2.8 29.3 + - - -
358A ALA* 1.3 76.6 + - - +
360A SER* 1.3 60.4 + - - +
395A PHE* 3.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 3.4 21.3 + - - -
167A THR* 4.0 4.1 - - - +
171A ILE* 4.7 2.0 - - - -
190A ASN* 3.6 2.5 + - - +
191A ALA* 3.6 4.2 - - - -
192A LEU* 2.9 37.7 + - - +
345A GLN* 3.0 31.0 + - - +
346A LYS 3.3 7.4 - - - -
347A VAL* 4.1 3.6 - - - -
359A SER* 1.3 77.4 - - - +
361A SER* 1.3 61.8 + - - +
362A THR* 3.9 4.4 + - - -
395A PHE* 3.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 3.3 26.8 - - - +
171A ILE* 4.1 10.8 - - - -
174A LEU* 3.3 38.5 - - - +
189A VAL* 4.1 1.7 - - - +
190A ASN 3.3 9.2 + - - -
191A ALA* 5.5 0.2 - - - -
344A LEU 4.1 0.5 - - - +
345A GLN* 3.3 2.0 - - - -
346A LYS* 2.8 37.3 + - - +
360A SER* 1.3 75.3 + - - +
362A THR* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.1 29.1 + - - +
62A VAL* 3.8 15.9 - - + -
65A VAL* 3.8 15.0 - - + +
66A LEU* 5.9 0.9 - - + -
189A VAL* 3.3 6.1 - - - +
190A ASN* 3.0 37.3 + - - -
309A LEU* 4.2 10.5 - - + -
344A LEU 3.5 11.0 - - - +
345A GLN* 3.2 26.9 + - + +
360A SER* 3.9 0.9 + - - -
361A SER* 1.3 73.1 - - - +
363A ALA* 1.3 64.8 + - - +
364A VAL* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 5.0 0.4 - - - -
174A LEU* 4.0 23.8 - - + -
175A LEU* 5.3 0.4 - - + -
187A VAL* 4.8 1.3 - - + -
188A LEU 3.1 9.2 - - - +
189A VAL* 4.3 7.0 - - + -
342A GLN 3.9 1.2 - - - +
343A ALA* 3.5 2.4 - - - -
344A LEU* 3.0 42.0 + - + +
361A SER 4.2 0.2 + - - -
362A THR* 1.3 78.0 - - - +
364A VAL* 1.3 64.5 + - - +
365A ILE* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.5 27.5 - - + +
66A LEU* 4.5 11.7 - - + -
69A LEU* 3.9 23.3 - - + -
186A LEU* 4.0 0.9 - - + +
187A VAL* 3.3 3.6 - - - -
188A LEU* 2.8 40.0 + - + +
309A LEU* 6.5 0.9 - - + -
313A LEU* 5.8 0.9 - - + -
321A MET* 5.0 3.8 - - + -
340A VAL* 3.5 31.9 - - + -
342A GLN 3.6 3.8 - - - +
343A ALA* 4.4 14.8 - - + -
362A THR* 6.1 1.8 - - + -
363A ALA* 1.3 75.1 - - - +
365A ILE* 1.3 61.7 + - - +
366A VAL* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.0 27.4 - - + -
179A ALA* 4.2 15.3 - - + +
180A VAL* 5.0 2.0 - - + -
184A THR* 4.0 22.0 - - + -
186A LEU 3.6 3.6 - - - +
187A VAL* 3.9 16.4 - - + -
340A VAL* 3.7 3.3 - - - -
341A ALA* 2.8 29.8 + - - +
342A GLN* 2.9 45.8 + - + +
344A LEU* 4.4 12.6 - - + -
363A ALA* 4.4 8.7 - - + -
364A VAL* 1.3 80.4 - - - +
366A VAL* 1.3 62.3 + - - +
368A ALA* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 4.8 1.1 - - - +
184A THR* 3.2 18.5 - - - +
185A ARG* 4.1 11.2 - - + +
186A LEU* 2.8 46.6 + - + +
329A PHE* 4.5 11.0 - - + -
338A LEU* 4.1 30.5 - - + -
339A HIS* 3.7 25.6 - - + +
340A VAL* 4.5 4.7 - - + -
364A VAL* 5.9 1.8 - - + +
365A ILE* 1.3 70.9 - - - +
367A SER* 1.3 78.7 + - - +
----------------------------------------------------------
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