Contacts of the strand formed by residues 429 - 437 (chain X) in PDB entry 4HSC
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 TYR 429 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167X ASP* 5.8 0.4 - - - +
344X TYR* 3.2 6.0 - - - -
345X GLY 2.8 39.5 + - - +
346X ARG* 3.4 36.9 + - - -
394X LEU 4.4 2.5 - - - -
395X GLY* 3.9 8.0 - - - +
396X GLY* 3.6 40.4 - - - -
400X GLU* 3.7 12.8 + - - -
427X PRO* 3.7 25.3 - - + +
428X ALA* 1.3 81.1 - - - +
430X PRO* 1.3 82.6 - - + +
431X ILE* 3.3 4.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 430 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165X ILE* 3.7 37.5 - - + +
167X ASP* 3.9 21.4 - - - +
170X THR* 5.2 4.3 - - - +
173X THR 5.7 4.0 - - - +
342X VAL* 4.2 3.1 - - + -
343X ALA 3.6 6.7 - - - +
344X TYR* 3.7 24.4 - - + -
396X GLY* 6.2 0.4 - - - -
428X ALA 4.9 0.2 - - - +
429X TYR* 1.3 94.2 - - + +
431X ILE* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 431 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164X SER* 3.4 6.9 - - - -
165X ILE* 3.0 25.5 + - - +
298X LYS* 4.3 14.0 - - + +
299X GLN 3.7 31.6 - - - +
300X ILE* 4.3 9.6 - - + -
343X ALA* 2.8 25.9 + - + +
344X TYR 4.2 1.8 - - - -
345X GLY 3.8 15.3 - - - +
346X ARG 3.8 12.6 - - - +
347X THR* 3.4 23.8 - - - +
429X TYR* 3.4 11.7 - - + +
430X PRO* 1.3 80.8 - - - +
432X SER* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162X ASP* 4.3 19.9 + - - +
163X ILE 3.0 19.3 - - - -
164X SER* 4.3 1.3 - - - -
165X ILE* 3.8 5.8 - - - +
251X GLN* 4.7 8.6 + - - -
298X LYS* 5.2 8.2 - - - +
300X ILE* 5.3 2.3 - - - +
342X VAL* 3.5 5.7 - - - +
343X ALA* 2.9 40.0 + - - +
431X ILE* 1.3 83.9 - - - +
433X TYR* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 433 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X VAL 3.6 1.9 - - - +
162X ASP* 3.6 1.0 - - - +
163X ILE* 2.9 48.8 + - + +
164X SER 4.3 4.9 - - - -
165X ILE* 3.4 27.6 - - + -
173X THR* 3.6 19.3 - - + -
179X GLN* 2.8 29.5 + - - -
185X PHE* 3.1 24.0 + + - -
188X ASN* 6.1 0.5 - - - -
190X PRO* 3.8 11.2 - - + +
339X VAL* 3.8 19.7 - - + -
341X ASN* 3.2 15.3 - - - +
342X VAL* 3.9 13.5 - - + +
343X ALA 4.7 0.4 - - - +
432X SER* 1.3 77.3 + - - +
434X THR* 1.3 64.3 + - - +
435X SER* 3.2 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X VAL* 3.5 25.6 - - + +
162X ASP* 3.6 17.9 - - - +
163X ILE* 5.6 0.2 - - - -
339X VAL* 3.6 4.3 - - - +
340X SER* 2.9 37.6 + - - -
341X ASN* 2.9 27.3 + - + +
433X TYR* 1.3 76.0 - - - +
435X SER* 1.3 68.4 + - - +
443X ILE* 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 435 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X VAL 4.7 1.0 + - - -
163X ILE* 6.1 1.0 - - - +
179X GLN* 4.8 0.3 + - - -
185X PHE* 4.0 11.6 - - - -
337X LEU* 4.3 15.9 - - - -
338X PHE 3.2 16.4 - - - -
339X VAL* 4.0 4.0 - - - +
340X SER 4.2 0.7 - - - +
433X TYR* 3.2 31.4 + - - -
434X THR* 1.3 74.8 + - - +
436X VAL* 1.3 62.9 + - - +
443X ILE* 3.6 4.2 - - - +
444X ALA* 2.7 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308X LEU* 3.8 21.8 - - + -
337X LEU* 3.4 5.4 - - - -
338X PHE* 2.7 48.2 + - + +
340X SER* 4.0 13.2 - - - +
435X SER* 1.3 77.3 - - - +
437X PHE* 1.3 63.2 + - - +
441X ASN* 3.6 40.4 - - - +
442X LYS 3.3 9.9 - - - +
443X ILE* 3.5 28.0 - - + -
444X ALA 4.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 437 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X TYR* 3.5 39.5 - + - +
120X GLU* 3.6 48.9 - - + -
123X VAL* 3.8 12.3 - - + -
124X LEU* 4.0 15.3 - - + -
181X ALA* 4.1 7.4 - - + -
335X PRO* 4.7 4.0 - - + -
336X PRO 3.7 8.1 - - - +
337X LEU* 3.6 16.1 - - + +
436X VAL* 1.3 69.9 - - - +
438X LEU* 1.3 59.2 + - - +
440X ASN* 3.1 14.2 + - + -
441X ASN* 2.6 34.3 + - - -
442X LYS 3.0 20.7 + - - -
443X ILE 4.2 3.8 - - - -
444X ALA* 3.8 19.1 - - + -
445X GLY 5.2 0.9 - - - -
----------------------------------------------------------
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