Contacts of the helix formed by residues 306 - 316 (chain B) in PDB entry 6R7X
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 PRO 306 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 6.3 1.1 - - + -
304B LEU 4.6 2.7 - - - +
305B TYR* 1.3 111.8 - - + +
307B SER* 1.3 64.9 + - - +
308B TYR* 3.3 31.2 - - + +
309B LYS* 3.4 34.1 + - + +
310B ARG* 3.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ARG* 5.7 3.2 + - - -
305B TYR 3.5 3.9 + - - -
306B PRO* 1.3 70.1 - - - +
308B TYR* 1.3 61.4 + - - +
310B ARG* 3.3 21.9 + - - +
311B GLN* 2.9 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO* 3.6 24.6 - - + +
307B SER* 1.3 77.0 - - - +
309B LYS* 1.3 95.7 + - + +
311B GLN* 3.8 6.5 - - - +
312B LEU* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TYR* 3.7 28.9 - - + +
306B PRO* 3.4 25.6 + - + +
307B SER 3.3 0.6 - - - -
308B TYR* 1.3 108.4 - - + +
310B ARG* 1.3 56.8 + - - +
312B LEU* 3.4 9.2 + - + +
313B ARG* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ARG* 5.7 4.8 - - - +
288B PHE* 4.0 5.9 - - - -
305B TYR* 3.8 35.2 + - + +
306B PRO 3.5 5.1 + - - +
307B SER* 3.3 27.5 + - - +
309B LYS* 1.3 79.5 - - - +
311B GLN* 1.3 63.8 + - - +
313B ARG* 3.3 4.9 + - - +
314B ILE* 2.9 41.3 + - + +
388B GLU 3.6 22.8 - - - +
389B ASN 3.0 20.9 + - - -
390B HIS* 4.0 21.4 + - + +
391B ARG* 4.6 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A UMQ 5.7 3.0 + - - -
307B SER* 2.9 31.2 + - - +
308B TYR* 3.9 6.5 - - - +
309B LYS 3.4 0.2 - - - -
310B ARG* 1.3 83.0 - - - +
312B LEU* 1.3 60.0 + - + +
314B ILE* 3.8 16.5 - - - +
315B TYR* 2.9 66.7 + - + +
399B HIS* 5.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B TYR* 2.9 30.7 + - + +
309B LYS* 3.7 8.7 - - + +
310B ARG 3.3 0.2 - - - -
311B GLN* 1.3 77.4 - - + +
313B ARG* 1.3 57.7 + - + +
315B TYR* 6.3 0.2 - - + -
316B LEU* 2.9 65.0 + - + +
317B VAL* 4.1 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B HIS* 5.1 7.7 - - - -
305B TYR* 2.6 39.6 + - - -
309B LYS* 2.9 22.6 + - + +
310B ARG* 3.7 5.4 - - - +
312B LEU* 1.3 76.9 - - + +
314B ILE* 1.3 63.7 + - - +
317B VAL* 3.5 21.0 - - + +
318B SER* 3.6 4.9 + - - -
387B TRP* 3.6 74.2 + - + +
388B GLU* 4.3 15.5 - - - +
389B ASN* 4.2 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG* 2.9 26.4 + - + +
311B GLN* 3.8 19.3 - - - +
313B ARG* 1.3 75.3 - - - +
315B TYR* 1.3 79.2 + - + +
316B LEU 3.1 4.2 + - - -
318B SER* 2.8 46.9 + - - +
319B LEU 3.4 2.4 + - - -
388B GLU* 3.4 23.8 - - + +
390B HIS* 4.1 8.3 - - + -
399B HIS* 3.6 31.0 - - + +
403B LYS* 5.3 0.9 - - - +
905B PC1 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A UMQ 5.1 13.4 - - + +
311B GLN* 2.9 48.0 + - + +
314B ILE* 1.3 79.5 - - + +
316B LEU* 1.3 70.7 + - + +
319B LEU* 4.5 26.1 - - + +
320B PRO* 4.5 8.2 - - - +
905B PC1 3.7 40.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 2.9 45.9 + - + +
315B TYR* 1.3 90.3 - - + +
317B VAL* 1.3 66.6 + - + +
320B PRO* 3.4 21.0 - - - +
----------------------------------------------------------
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