Contacts of the helix formed by residues 69 - 79 (chain B) in PDB entry 6EBT
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 GLY 69 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.5 17.9 - - - -
62B VAL* 4.1 5.6 - - - -
68B TYR* 1.3 74.6 - - - +
70B ALA* 1.3 66.8 + - - -
72B THR* 3.3 2.1 + - - -
73B VAL* 3.1 24.9 + - - +
155B GLU* 2.7 27.4 + - - +
159B ASN* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.2 31.8 + - + +
54B TYR 4.2 21.5 - - - +
55B ASP* 4.3 6.7 - - + +
60B LEU* 3.3 24.8 - - + +
62B VAL* 4.5 2.2 - - - -
69B GLY* 1.3 72.7 - - - -
71B GLN* 1.3 60.1 + - + +
73B VAL* 3.1 4.7 + - - -
74B ARG* 2.7 27.1 + - - +
155B GLU* 3.5 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 5.2 11.2 - - + +
70B ALA* 1.3 77.5 - - + +
72B THR* 1.3 57.7 + - - +
74B ARG* 3.3 9.4 + - - +
75B SER* 2.9 31.5 + - - -
151B MET* 3.3 49.4 - - + +
154B ASN* 6.1 0.2 - - - +
155B GLU* 3.0 22.3 + - - +
177B PRO* 5.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.6 28.5 - - + +
69B GLY 3.6 3.8 - - - -
71B GLN* 1.3 77.4 - - - +
73B VAL* 1.3 64.2 + - - +
75B SER* 3.1 9.2 + - - -
76B THR* 3.0 25.5 + - - +
137B PRO* 3.8 16.2 - - + -
138B LEU* 4.2 7.6 - - + -
148B GLN 5.7 0.7 - - - -
151B MET* 5.7 0.4 - - - +
152B ASN* 3.3 44.3 + - - +
155B GLU* 2.7 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.2 22.4 - - + -
61B LYS 3.9 17.7 - - - +
62B VAL* 3.9 18.2 - - + -
63B PRO* 5.0 1.6 - - + -
68B TYR* 3.7 23.3 - - + -
69B GLY 3.1 15.4 + - - +
70B ALA* 3.5 7.6 - - - +
72B THR* 1.3 73.9 - - - +
74B ARG* 1.3 62.7 + - - +
76B THR* 2.4 29.4 + - - +
77B MET* 3.2 15.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 2.6 44.1 + - - +
57B PHE* 3.4 40.4 + - + +
58B GLY 3.8 3.0 + - - +
59B GLU 4.8 0.4 + - - -
60B LEU* 3.7 22.8 - - + +
70B ALA 2.7 17.1 + - - +
71B GLN* 3.4 11.9 - - - +
72B THR 3.2 0.2 - - - -
73B VAL* 1.3 73.4 - - - +
75B SER* 1.3 61.7 + - - +
77B MET* 3.1 41.2 + - - +
78B ASN* 3.3 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN 2.9 15.5 + - - -
72B THR* 3.1 4.8 + - - -
74B ARG* 1.3 77.5 - - - +
76B THR* 1.3 62.1 + - - +
78B ASN* 5.1 1.3 - - - +
79B PHE* 3.2 33.4 + - - +
138B LEU* 3.5 24.8 - - - +
148B GLN* 3.1 42.9 + - - +
151B MET* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 5.9 2.0 - - + +
72B THR 3.0 14.1 + - - +
73B VAL* 2.4 28.2 + - - +
75B SER* 1.3 76.0 - - - +
77B MET* 1.3 59.7 + - - +
79B PHE 4.2 6.4 + - - +
80B LYS* 3.2 23.2 - - - +
137B PRO* 3.7 29.2 - - + +
138B LEU* 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.5 22.4 - - + -
73B VAL* 3.3 16.2 - - + +
74B ARG* 3.1 49.4 + - - +
76B THR* 1.3 82.2 - - - +
78B ASN* 1.3 65.7 + - - +
79B PHE 3.5 0.2 - - - -
80B LYS* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.3 37.0 + - - +
75B SER* 3.5 1.0 + - - +
77B MET* 1.3 85.3 - - - +
79B PHE* 1.3 85.2 + - + +
80B LYS 3.8 1.6 - - - -
81B ILE* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.2 20.0 + - - +
76B THR* 4.3 4.3 - - - +
77B MET 3.5 0.2 - - - -
78B ASN* 1.3 100.5 - - + +
80B LYS* 1.3 61.8 + - - +
81B ILE* 3.3 18.6 + - + -
138B LEU* 6.4 0.2 - - + -
139B VAL* 3.5 19.1 - - + +
141B TRP 3.3 25.6 - - - +
142B GLN* 3.7 19.5 - - + -
143B THR* 4.4 8.3 - - + -
148B GLN* 3.2 38.8 - - - +
----------------------------------------------------------
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