Contacts of the helix formed by residues 130 - 139 (chain W) in PDB entry 6FF7
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 HIS 130 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128W LYS 3.3 0.6 + - - -
129W LYS* 1.3 75.4 - - + +
131W TYR* 1.3 64.2 + - - +
132W ARG 3.3 3.1 - - - -
133W LEU* 3.2 13.5 + - + +
134W TYR* 2.9 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103W LEU* 6.0 4.0 - - - -
125W VAL 3.6 20.9 - - - +
126W THR* 3.8 15.0 - - - +
128W LYS* 3.2 19.9 + - + +
129W LYS 3.2 2.1 + - - -
130W HIS* 1.3 75.0 - - - +
132W ARG* 1.3 63.3 + - - +
134W TYR* 3.4 6.2 + - - +
135W VAL* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130W HIS 3.3 0.8 - - - -
131W TYR* 1.3 76.9 - - - +
133W LEU* 1.3 63.6 + - - +
135W VAL* 3.2 8.0 + - - +
136W ILE* 3.1 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130W HIS* 3.2 16.0 + - + +
132W ARG* 1.3 76.1 - - - +
134W TYR* 1.3 64.2 + - - +
136W ILE* 3.2 4.8 + - - -
137W TYR* 3.1 21.9 + - - +
154W GLU* 5.3 4.5 - - + +
157W GLU* 5.3 3.6 - - + +
158W ALA* 3.6 29.8 - - + +
161W MET* 5.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103W LEU* 4.9 16.2 - - + -
130W HIS* 2.9 21.1 + - + +
131W TYR* 3.6 7.0 - - - +
133W LEU* 1.3 77.2 - - - +
135W VAL* 1.3 62.9 + - - +
137W TYR* 3.5 3.9 + - - +
138W LYS* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131W TYR 3.1 13.1 + - - +
132W ARG* 3.2 7.8 + - - +
134W TYR* 1.3 76.9 - - - +
136W ILE* 1.3 58.6 + - - +
138W LYS* 5.0 2.0 - - - -
139W VAL* 2.7 40.6 + - + +
142W VAL* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132W ARG 3.1 13.4 + - - +
133W LEU* 3.2 10.5 + - - +
135W VAL* 1.3 77.0 - - - +
137W TYR* 1.3 60.6 + - - +
139W VAL 4.7 3.4 - - - -
140W PRO* 3.3 26.2 - - - +
142W VAL* 6.3 1.1 - - - -
150W VAL* 5.6 9.6 - - + -
154W GLU* 5.1 11.4 - - + +
155W ARG* 5.3 7.0 - - + -
158W ALA* 4.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133W LEU 3.1 15.5 + - - +
134W TYR* 4.1 3.1 - - - +
136W ILE* 1.3 77.3 - - - +
138W LYS* 1.3 61.4 + - - +
139W VAL 3.6 0.2 + - - -
140W PRO* 4.1 8.4 - - - +
158W ALA* 3.8 27.3 - - + +
162W PHE* 4.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W LEU 6.4 0.2 - - - -
107W ASP* 5.6 9.9 - - + -
110W ALA* 3.1 29.0 - - + +
134W TYR 3.0 18.1 + - - +
135W VAL* 4.4 2.0 - - - +
137W TYR* 1.3 77.2 - - - +
139W VAL* 1.3 57.5 + - + +
140W PRO 3.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109W LEU* 4.6 22.4 - - + +
110W ALA* 4.6 5.6 - - - +
135W VAL* 2.7 26.4 + - + +
136W ILE* 4.0 2.3 - - - +
138W LYS* 1.3 76.0 - - + +
140W PRO* 1.3 61.0 - - - +
141W GLN* 3.1 6.3 + - + +
142W VAL* 3.1 24.4 + - + +
----------------------------------------------------------
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