Contacts of the helix formed by residues 295 - 303 (chain B) in PDB entry 4XZC
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 SER 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 5.6 1.1 - - - -
241B GLU* 3.7 21.5 - - - -
291B LEU 3.2 9.7 + - - -
292B ALA* 3.8 5.6 + - - -
294B LYS* 1.3 78.0 - - - +
296B SER* 1.3 65.0 + - - +
297B ALA 3.9 1.3 - - - -
298B LEU* 3.5 38.7 - - - +
299B ARG* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 4.8 20.9 - - - -
179B ILE 5.0 7.6 - - - -
294B LYS 3.2 4.0 + - - -
295B SER* 1.3 71.3 - - - +
297B ALA* 1.3 61.9 + - - +
299B ARG* 3.3 21.5 + - - +
300B ALA* 3.2 20.0 + - - +
375B TYR* 3.5 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 5.1 22.4 - - - +
241B GLU* 3.7 33.0 - - + +
295B SER* 3.1 1.0 - - - -
296B SER* 1.3 79.8 - - - +
298B LEU* 1.3 61.9 + - + +
299B ARG 3.4 0.2 - - - -
300B ALA* 3.6 6.2 + - - +
301B GLN* 3.3 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 5.4 0.2 - - - +
240B ALA* 5.1 2.2 - - + +
241B GLU* 4.1 33.2 - - + +
245B HIS* 4.0 22.4 - - + -
292B ALA* 3.1 31.9 - - + +
295B SER* 3.2 21.8 + - - +
297B ALA* 1.3 78.1 - - - +
299B ARG* 1.3 59.4 + - - +
300B ALA 3.2 1.6 - - - -
301B GLN* 3.7 25.0 + - - +
302B GLY* 3.2 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 5.4 8.7 - - - -
118B PRO* 5.5 4.9 - - + -
120B PRO* 6.0 6.1 - - + -
123B LEU* 4.0 20.5 - - + +
294B LYS* 3.6 17.6 + - - +
295B SER 3.2 19.1 + - - +
296B SER* 3.3 15.2 + - - +
298B LEU* 1.3 76.9 - - - +
300B ALA* 1.3 58.5 + - - +
302B GLY* 3.7 1.7 - - - +
303B ALA* 3.2 25.1 + - - +
375B TYR* 3.3 55.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 5.8 6.1 - - - +
296B SER 3.2 15.7 + - - +
297B ALA* 3.8 8.5 - - - +
298B LEU 3.2 0.4 - - - -
299B ARG* 1.3 76.2 - - - +
301B GLN* 1.3 62.1 + - + +
302B GLY 3.0 5.2 + - - -
303B ALA* 3.5 9.8 + - - +
304B GLN* 3.5 12.1 + - - +
375B TYR* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLN* 4.1 0.2 + - - -
241B GLU* 4.2 14.9 + - - +
297B ALA* 3.3 23.0 + - - +
298B LEU* 3.7 23.2 + - - +
300B ALA* 1.3 78.0 - - + +
302B GLY* 1.3 60.8 + - - +
304B GLN* 3.5 23.7 + - - +
470B ALA 6.1 0.4 - - - +
471B TYR* 3.1 39.9 - - + +
473B VAL 4.7 14.7 + - - +
474B LYS* 5.6 1.6 - - - -
475B GLY 3.8 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.6 32.4 - - - +
124B VAL* 6.0 0.9 - - - -
127B GLN* 2.8 23.2 + - - +
298B LEU 3.2 17.3 + - - -
299B ARG 3.6 2.9 + - - -
300B ALA 3.0 1.2 - - - -
301B GLN* 1.3 78.6 - - - +
303B ALA* 1.3 53.9 + - - +
304B GLN 3.3 2.0 - - - -
378B PRO* 4.2 1.6 - - - +
471B TYR* 4.2 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 5.5 0.9 - - + -
123B LEU* 3.8 17.3 - - + -
299B ARG 3.2 18.0 + - - +
300B ALA* 3.5 4.6 + - - +
302B GLY* 1.3 74.8 - - - +
304B GLN* 1.3 62.2 + - - +
305B ILE* 3.3 8.1 + - - +
374B LEU 4.4 13.0 - - - +
375B TYR* 4.6 7.4 - - + -
376B MET 4.2 10.8 - - - +
378B PRO* 3.5 21.9 - - + +
----------------------------------------------------------
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