Contacts of the helix formed by residues 321 - 326 (chain B) in PDB entry 1X7W
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 321 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PRO* 3.8 28.0 - - + +
319B HIS 3.2 1.2 - - - -
320B ILE* 1.3 98.6 - - + +
322B GLU* 1.3 66.5 + - - +
323B PRO* 3.3 3.8 - - - -
324B PHE* 2.9 34.0 + + + +
325B TYR* 3.2 9.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 3.3 21.2 - - - +
139B VAL 4.4 0.7 + - - -
140B GLY* 2.9 52.2 + - - +
141B HIS* 3.2 5.5 + - - -
142B GLY 4.0 3.3 + - - -
192B ILE* 5.7 0.2 - - - +
317B PHE* 3.3 28.9 - - + -
318B PRO* 3.9 10.8 + - - +
319B HIS 3.3 12.1 + - - +
320B ILE 3.3 1.6 - - - -
321B PHE* 1.3 75.4 - - - +
323B PRO* 1.3 66.5 - - + +
325B TYR* 2.8 24.4 + - - -
326B ILE* 3.3 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY 5.4 2.5 - - - +
319B HIS 5.0 0.4 - - - +
320B ILE 3.6 11.7 - - - +
321B PHE 3.3 4.7 - - - -
322B GLU* 1.3 95.8 - - + +
324B PHE* 1.3 71.7 + - + +
325B TYR 3.4 0.2 - - - -
326B ILE* 3.9 18.8 - - + +
328B ASP* 4.2 11.3 - - - +
331B LYS* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 3.3 10.3 + - - -
320B ILE 5.3 2.7 - - - -
321B PHE* 2.9 35.6 + + + +
323B PRO* 1.3 90.7 - - + +
325B TYR* 1.3 58.4 + - - +
331B LYS* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU 3.7 7.2 - - - -
282B PRO* 3.5 18.5 - - - +
311B CYS 4.7 1.4 - - - +
312B GLY* 3.4 23.1 - - - -
313B TYR* 2.7 56.3 + + + -
315B THR* 3.2 31.3 + - - -
316B PRO 4.2 2.7 - - - -
317B PHE* 3.5 38.6 - + - -
318B PRO* 3.7 24.2 - - + -
321B PHE* 3.2 9.4 + - + +
322B GLU* 2.8 12.8 + - - +
324B PHE* 1.3 79.4 - - - +
326B ILE* 1.3 67.5 + - + +
327B PRO* 3.7 1.1 - - + -
331B LYS* 3.8 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 4.2 16.8 - - - -
280B GLU* 5.6 2.9 - - + -
317B PHE* 4.0 26.9 - - + -
322B GLU* 3.6 24.2 - - + +
323B PRO* 3.9 16.1 - - + +
324B PHE 4.8 0.2 - - - -
325B TYR* 1.3 79.3 - - + +
327B PRO* 1.3 68.5 - - + +
328B ASP* 2.8 31.0 + - + +
331B LYS* 3.3 17.4 + - - +
----------------------------------------------------------
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