Contacts of the strand formed by residues 355 - 363 (chain B) in PDB entry 1HQR
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 PHE 355 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP 5.6 5.2 - - - -
29A ASP* 5.2 5.4 - - - -
321B GLY* 3.1 24.4 + - - -
322B PHE* 2.6 41.5 + - + -
323B TYR* 3.8 24.2 - + - -
324B PRO 4.2 0.2 - - - -
325B GLY* 3.5 24.2 - - - -
347B LEU* 3.0 41.3 - - + -
348B ILE 3.4 18.8 - - - +
349B GLN* 4.4 20.6 - - + -
350B ASN* 3.5 5.0 - - - +
354B THR* 1.3 79.0 - - - +
356B GLN* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 5.0 8.2 - - - +
93A THR* 3.1 34.1 + - - +
94A ASN* 4.1 2.0 + - - +
106A ILE* 4.3 4.8 - - - +
319B VAL 3.0 14.6 - - - +
320B ASN* 3.7 18.2 - - - +
321B GLY 4.8 0.4 - - - +
322B PHE* 3.3 2.2 - - - -
346B GLY 3.7 0.5 - - - +
347B LEU* 4.1 1.0 - - - -
348B ILE* 3.2 43.0 + - + +
350B ASN* 3.0 35.2 + - - +
355B PHE* 1.3 79.1 - - - +
357B THR* 1.3 68.6 + - - +
358B LEU* 4.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B CYS 3.6 1.0 - - - +
319B VAL* 2.8 45.7 + - + +
322B PHE* 3.8 19.7 - - + -
327B ILE* 4.7 9.9 - - + -
329B VAL* 4.8 6.1 - - + -
344B SER* 3.6 14.4 + - - -
345B THR* 3.3 8.3 + - - -
346B GLY 3.1 21.2 + - - -
347B LEU* 4.6 2.0 - - + -
348B ILE* 5.2 0.7 - - - -
356B GLN* 1.3 79.8 - - - +
358B LEU* 1.3 71.8 + - - +
359B VAL* 4.3 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 3.8 22.0 - - - +
316B VAL* 5.6 0.4 - - + -
317B CYS 3.2 8.1 - - - +
318B SER* 3.2 25.6 - - - +
320B ASN* 4.8 0.4 - - - +
344B SER* 3.3 2.3 - - - -
345B THR* 2.9 49.6 + - + +
348B ILE* 6.0 1.6 - - + -
356B GLN* 4.6 12.3 - - + +
357B THR* 1.3 106.7 + - - +
359B VAL* 1.3 62.5 + - - +
360B MET* 3.9 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 3.6 0.5 - - - -
317B CYS* 3.0 41.5 + - + +
319B VAL* 6.1 0.2 - - + -
329B VAL* 3.5 37.7 - - + +
331B TRP* 3.4 27.6 + - + +
342B VAL* 4.7 4.0 - - + -
343B VAL 3.3 5.4 - - - +
344B SER* 3.7 22.4 - - - +
357B THR* 4.7 4.3 - - - +
358B LEU* 1.3 72.8 - - - +
360B MET* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 5.7 0.9 - - - +
304B ALA* 5.8 7.0 - - + -
314B LEU* 6.4 2.9 - - + -
315B LEU 3.3 7.6 - - - +
316B VAL* 4.1 16.6 - - + -
341B GLY 3.9 0.5 - - - +
342B VAL* 3.0 7.4 - - - +
343B VAL* 2.5 55.7 + - + +
344B SER* 5.1 0.4 - - - -
345B THR* 4.9 6.7 - - + -
358B LEU* 4.0 31.0 - - + +
359B VAL* 1.3 77.0 - - - +
361B LEU* 1.3 62.4 + - - +
362B GLU* 5.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 4.1 5.0 - - - +
315B LEU* 2.8 44.8 + - + +
331B TRP* 3.3 50.9 - - + +
338B GLU* 4.4 11.9 - - + +
340B ALA 5.0 3.1 - - - +
341B GLY 4.5 1.6 - - - +
342B VAL* 3.3 28.2 - - + +
359B VAL 3.7 1.6 + - - -
360B MET* 1.3 74.0 - - - +
362B GLU* 1.3 76.9 + - - +
363B THR* 3.1 38.4 + - + +
371B TYR* 5.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 6.0 5.2 - - + -
313B ASN 4.2 6.5 - - - +
314B LEU* 5.4 6.7 - - + -
341B GLY* 3.2 22.9 + - - +
360B MET 5.2 1.1 - - - +
361B LEU* 1.3 77.6 - - - +
363B THR* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 4.5 2.0 - - - +
313B ASN* 2.7 42.6 + - - +
315B LEU* 5.6 3.0 - - - +
333B ARG* 3.7 29.2 - - - +
338B GLU* 6.3 0.2 - - + -
361B LEU* 3.1 26.9 + - + +
362B GLU* 1.3 79.0 - - - +
364B VAL* 1.3 59.4 + - - +
371B TYR* 3.1 30.3 - - + -
----------------------------------------------------------
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