Contacts of the helix formed by residues 131 - 140 (chain A) in PDB entry 6B9H
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 GLN 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 6.1 0.4 - - - +
48A ILE 4.7 6.5 - - - +
129A CYS* 3.1 9.5 - - - -
130A GLU* 1.3 93.3 + - + +
132A LYS* 1.3 64.4 + - - +
133A GLN 3.2 2.9 - - - -
134A GLU* 3.0 38.3 + - + +
135A TYR* 3.1 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 5.2 7.7 - - - +
126A ALA 3.4 11.9 - - - +
127A VAL* 3.3 32.7 + - - +
128A ASN* 4.0 16.8 + - - -
129A CYS 3.0 19.1 + - - +
130A GLU 3.3 3.3 - - - +
131A GLN* 1.3 77.0 - - - +
133A GLN* 1.3 68.7 + - + +
135A TYR* 3.2 0.7 + - - -
136A ILE* 2.9 35.3 + - + +
451B LEU 5.8 3.5 + - - -
452B LEU* 6.0 1.1 - - + -
454B LYS 5.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU 5.0 0.6 + - - +
131A GLN 3.1 1.0 + - - -
132A LYS* 1.3 84.6 - - + +
134A GLU* 1.3 71.7 + - - +
136A ILE* 3.8 1.4 - - - +
137A GLN* 2.9 62.1 + - - +
452B LEU* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU 4.7 1.2 - - - +
131A GLN* 3.0 40.9 + - + +
133A GLN* 1.3 91.6 - - - +
135A TYR* 1.3 66.5 + - + +
137A GLN* 3.8 15.1 - - - +
138A ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 5.0 6.4 + + + -
23A PHE* 3.6 33.5 - + - -
47A LYS* 3.3 25.6 + - - +
48A ILE* 3.4 15.3 + - + -
126A ALA* 3.5 34.3 - - + +
127A VAL* 5.0 3.6 - - + +
129A CYS* 3.8 17.3 - - - -
131A GLN* 3.1 33.6 + - + +
132A LYS 3.8 4.9 - - - +
134A GLU* 1.3 78.6 - - + +
136A ILE* 1.3 63.2 + - - +
138A ALA* 3.3 8.8 + - + +
139A ILE* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 4.1 32.8 - - + +
132A LYS* 2.9 29.0 + - + +
133A GLN 3.8 3.1 - - - +
135A TYR* 1.3 75.0 - - - +
137A GLN* 1.3 64.5 + - - +
139A ILE* 3.2 10.4 + - + +
140A MET* 3.1 29.0 + - - +
154A ILE* 5.8 0.2 - - + -
448B PHE* 3.8 40.4 - - + +
451B LEU* 4.1 28.3 - - + +
452B LEU* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLN* 2.9 53.2 + - + +
134A GLU* 3.8 17.3 - - - +
136A ILE* 1.3 74.7 - - - +
138A ALA* 1.3 61.6 + - - +
140A MET* 3.3 21.7 + - - +
141A MET* 3.4 17.0 - - - +
452B LEU* 4.6 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 6.2 1.1 - - + +
22A THR* 6.0 2.9 - - - +
134A GLU 3.0 17.6 + - - +
135A TYR* 3.6 9.9 - - + +
136A ILE 3.2 0.2 - - - -
137A GLN* 1.3 73.8 - - - +
139A ILE* 1.3 66.9 + - + +
141A MET* 2.9 25.1 + - - +
142A MET* 3.7 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.8 32.8 - - + +
123A LEU* 4.0 12.1 - - + -
127A VAL* 4.3 15.0 - - + -
135A TYR* 3.1 18.1 + - + +
136A ILE* 3.2 10.1 + - + +
138A ALA* 1.3 74.4 - - + +
140A MET* 1.3 58.2 + - - +
142A MET* 2.9 29.7 + - - +
147A GLN* 3.4 14.8 - - + +
150A VAL* 3.9 29.6 - - + -
154A ILE* 5.0 1.8 - - + -
448B PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.1 23.0 + - - +
137A GLN* 3.5 18.2 - - - +
138A ALA 3.1 0.6 - - - -
139A ILE* 1.3 75.3 - - - +
141A MET* 1.3 64.3 + - - +
142A MET 3.4 0.4 - - - -
147A GLN* 3.1 22.5 + - - +
445B ALA* 3.9 25.8 - - + -
448B PHE* 3.7 35.4 - - + -
449B ASN* 3.8 24.0 - - - +
452B LEU* 4.4 5.8 - - - -
----------------------------------------------------------
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