Contacts of the helix formed by residues 7 - 16 (chain 2) in PDB entry 6Q8W
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 LYS 7 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 PHE* 3.8 34.5 + - + +
42 PHE* 3.8 18.3 + - + +
52 ASP 3.5 1.0 - - - -
62 ASP* 1.3 85.1 + - - +
82 GLN* 1.3 62.4 + - - +
92 ASP* 3.5 13.9 - - - +
102 PHE* 3.9 20.6 - - + -
112 LEU* 3.1 23.4 + - - +
332 ARG* 3.2 47.2 - - - +
372 GLU* 4.3 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 PHE 4.8 1.4 + - - -
52 ASP* 3.8 20.4 + - - +
62 ASP 3.4 4.9 + - - +
72 LYS* 1.3 71.6 - - - +
92 ASP* 1.3 67.1 + - - +
102 PHE 3.2 1.6 - - - -
112 LEU* 3.1 25.2 + - + +
122 GLU* 2.9 32.0 + - + +
522 LEU* 5.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 LYS* 3.5 11.4 - - - +
82 GLN* 1.3 82.5 + - - +
102 PHE* 1.3 62.3 + - - +
122 GLU* 3.5 5.7 + - - +
132 GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 10 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 PHE* 3.9 11.4 - + - -
72 LYS* 3.9 22.7 - - + -
82 GLN 3.2 0.4 - - - -
92 ASP* 1.3 81.7 + - - +
112 LEU* 1.3 67.4 + - + +
132 GLU* 3.6 16.4 - - + +
142 THR* 2.9 49.7 + - + +
172 LYS* 5.6 1.3 - - - -
292 PRO* 4.9 9.0 - - + -
302 LEU* 3.6 26.5 - - + -
332 ARG* 3.4 48.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 PHE* 3.4 47.6 - - + +
72 LYS 3.1 12.6 - - - +
82 GLN* 3.1 29.9 + - - +
102 PHE* 1.3 77.6 - - + +
122 GLU* 1.3 58.1 + - + +
142 THR* 2.8 17.8 + - - -
152 PHE* 2.9 39.0 + - + -
302 LEU* 3.8 17.7 - - + -
522 LEU* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 GLN* 2.9 23.4 + - + +
92 ASP* 3.8 6.1 - - - +
112 LEU* 1.3 76.4 - - + +
132 GLU* 1.3 64.1 + - - +
152 PHE* 4.6 3.4 - - - +
162 ALA* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501 LYS* 5.3 9.0 + - - -
92 ASP 2.9 19.5 + - - +
102 PHE* 3.2 17.4 + - + +
122 GLU* 1.3 77.3 - - - +
142 THR* 1.3 60.9 + - + +
162 ALA* 4.0 4.3 + - - +
172 LYS* 3.1 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 PHE* 2.9 50.4 + - + +
112 LEU* 2.8 19.9 + - - -
132 GLU* 1.3 76.2 - - + +
152 PHE* 1.3 64.5 + - - +
172 LYS* 3.0 38.1 + - - +
182 TYR* 3.1 27.1 - - - -
262 ALA* 4.9 3.5 - - - +
292 PRO* 5.1 10.5 - - + -
302 LEU* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 LEU* 2.9 44.0 + - + +
122 GLU* 4.3 2.7 - - - +
142 THR* 1.3 80.4 + - - +
162 ALA* 1.3 57.7 + - - +
172 LYS 3.2 0.2 - - - -
182 TYR* 3.3 24.9 + + - +
192 PRO 5.0 0.9 - - - +
202 PRO* 5.9 0.9 - - - +
232 ARG* 3.3 70.9 - - + +
262 ALA* 3.4 10.3 - - + -
302 LEU* 3.8 29.4 - - + -
522 LEU* 4.3 22.2 - - + -
532 VAL* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1721 HIS* 5.5 1.9 - - - -
122 GLU* 2.9 20.2 + - + +
132 GLU* 4.3 4.7 - - - +
152 PHE* 1.3 74.6 - - - +
172 LYS* 1.3 63.2 + - + +
182 TYR 3.2 5.6 + - - +
----------------------------------------------------------
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