Contacts of the helix formed by residues 130 - 141 (chain Q) in PDB entry 6VEN
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 VAL 130 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P MET* 4.7 20.6 - - + -
141P ILE* 5.6 5.8 - - + -
149P PRO* 4.6 8.1 - - + -
150P LEU* 3.9 30.3 - - + -
127Q ASN 4.7 2.0 - - - +
129Q ASN* 1.3 106.9 - - + +
131Q THR* 1.3 67.7 + - + +
132Q PRO* 3.4 3.8 - - - -
133Q HIS* 3.4 6.6 + - - +
134Q LEU* 3.0 30.8 + - + +
157Q LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ASN* 6.0 0.7 - - - +
74O PHE* 4.1 15.2 - - - -
75O PHE* 5.4 4.3 - - + -
490O ILE* 6.1 6.3 - - + -
494O ILE* 3.5 31.4 - - + +
127Q ASN* 2.5 52.0 + - + +
130Q VAL* 1.3 77.4 - - + +
132Q PRO* 1.3 61.0 - - - +
134Q LEU* 3.3 6.9 + - - +
135Q LEU* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 132 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O PHE* 3.5 34.7 - - + -
127Q ASN 3.9 5.2 - - - +
128Q THR 5.1 2.9 - - - +
129Q ASN 4.7 1.8 - - - +
130Q VAL* 3.5 5.8 - - - +
131Q THR* 1.3 95.9 - - - +
133Q HIS* 1.3 78.0 + - + +
135Q LEU* 3.4 6.9 + - + +
136Q ALA* 2.9 31.4 + - - +
139Q ARG* 4.4 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 133 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150P LEU* 3.2 34.7 - - + +
129Q ASN* 3.3 27.5 + - - -
130Q VAL* 3.8 7.5 - - + +
131Q THR 3.4 0.2 - - - -
132Q PRO* 1.3 89.7 - - + +
134Q LEU* 1.3 58.2 + - - +
137Q GLY* 2.9 24.4 + - - -
157Q LEU* 4.7 3.1 - - + +
160Q GLN* 3.0 51.1 + - + +
161Q SER* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491O VAL* 3.9 26.9 - - + -
494O ILE* 3.7 28.3 - - + -
495O ILE* 6.5 0.2 - - + -
134P LEU* 4.9 20.6 - - + -
138P MET* 4.9 14.1 - - + -
130Q VAL* 3.0 24.5 + - + +
131Q THR* 3.7 5.2 - - - +
133Q HIS* 1.3 74.8 - - - +
135Q LEU* 1.3 59.3 + - - +
137Q GLY* 3.2 1.9 + - - +
138Q MET* 2.9 37.5 + - + +
157Q LEU* 4.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O PHE* 3.7 39.3 - - + +
75O PHE* 5.2 5.2 - - + -
494O ILE* 3.6 37.2 - - + +
497O GLU* 4.9 15.3 - - + +
498O LEU* 5.9 0.7 - - + -
131Q THR* 2.9 24.5 + - - +
132Q PRO* 3.8 6.3 - - + +
134Q LEU* 1.3 76.4 - - - +
136Q ALA* 1.3 57.2 + - - +
138Q MET* 3.1 15.0 - - + +
139Q ARG* 2.9 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Q PRO 2.9 13.8 + - - +
135Q LEU* 1.3 76.7 - - - +
137Q GLY* 1.3 55.6 + - - +
139Q ARG* 3.5 21.1 + - - +
140Q LEU* 2.9 27.7 + - - +
156Q TYR* 3.5 16.4 + - - +
160Q GLN* 3.1 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q HIS 2.9 14.8 + - - -
134Q LEU* 3.2 4.0 + - - -
136Q ALA* 1.3 77.9 - - - +
138Q MET* 1.3 57.4 + - - +
140Q LEU* 3.2 6.6 + - - +
141Q ILE* 3.0 29.8 + - - +
153Q LEU* 5.5 6.5 - - - +
156Q TYR* 3.5 23.3 - - - -
157Q LEU* 5.9 3.8 - - - -
160Q GLN* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 138 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494O ILE* 3.2 42.4 - - - +
495O ILE* 3.4 28.5 - - + +
497O GLU* 5.0 0.2 - - + -
498O LEU* 3.5 36.9 - - + +
126P LEU* 4.8 18.2 - - + +
134Q LEU* 2.9 25.4 + - + +
135Q LEU* 3.1 21.5 - - + +
137Q GLY* 1.3 72.8 - - - +
139Q ARG* 1.3 60.1 + - - +
141Q ILE* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498O LEU* 3.8 26.7 - - + -
132Q PRO* 4.4 3.6 + - - +
135Q LEU* 2.9 34.0 + - - +
136Q ALA* 3.5 31.6 - - - +
138Q MET* 1.3 74.1 - - - +
140Q LEU* 1.3 66.0 + - - +
141Q ILE 3.2 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Q ALA 2.9 14.8 + - - +
137Q GLY* 3.2 10.3 + - - +
139Q ARG* 1.3 77.5 - - - +
141Q ILE* 1.3 69.0 + - + +
152Q VAL* 4.5 21.5 - - + +
153Q LEU* 5.4 1.6 - - - -
156Q TYR* 3.5 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P THR* 6.1 1.1 - - - +
125P TYR* 3.8 20.6 - - + +
126P LEU* 3.7 27.1 - - + -
130P VAL* 4.4 10.3 - - + -
137Q GLY 3.0 15.7 + - - +
138Q MET* 2.9 23.0 - - - +
139Q ARG* 3.2 6.8 - - - +
140Q LEU* 1.3 86.5 - - + +
148Q ASP* 5.3 11.9 - - + +
149Q PRO 5.7 0.4 - - - +
150Q LEU* 5.8 0.2 - - - -
152Q VAL* 4.6 18.2 - - + -
153Q LEU* 3.5 42.4 - - + -
----------------------------------------------------------
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