Contacts of the helix formed by residues 65 - 76 (chain B) in PDB entry 1D8L
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 ASN 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.8 14.1 - - - -
63B PHE* 3.3 8.9 - - - +
64B ASN* 1.3 82.7 - - - +
66B LYS* 1.3 64.6 + - - +
67B GLN* 2.9 48.7 + - - +
68B GLU* 3.0 42.1 + - - +
69B ARG* 3.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.6 33.7 - - - +
48B PHE* 3.6 42.5 - - + -
65B ASN* 1.3 73.9 - - - +
67B GLN* 1.3 74.2 + - - +
69B ARG* 3.2 22.4 + - - +
70B THR* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASN* 2.9 29.1 + - - +
66B LYS* 1.3 87.3 - - - +
68B GLU* 1.3 61.3 + - + +
70B THR* 3.5 6.4 + - - +
71B LEU* 3.1 22.0 + - - +
137B GLY* 4.4 5.4 - - - -
138B ASP* 3.1 45.6 + - - +
139B LEU* 3.3 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO* 5.6 0.8 - - + +
33B THR* 5.6 2.3 + - - -
34B CYS* 3.3 21.8 + - - -
63B PHE* 3.9 14.1 - - + -
64B ASN* 3.0 30.9 + - - +
65B ASN* 3.0 31.3 + - - +
66B LYS 3.3 0.2 - - - -
67B GLN* 1.3 73.3 - - + +
69B ARG* 1.3 59.4 + - - +
71B LEU* 3.3 7.5 + - - +
72B PHE* 2.9 29.1 + - - +
90B LEU* 4.2 13.7 - - + +
95B ALA* 4.5 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.1 4.8 + - - -
13A GLN* 6.0 2.6 - - - +
16A LEU* 6.2 1.2 - - - +
18A LEU* 6.0 2.4 - - - +
27A GLU* 3.6 20.6 + - - -
3B GLY* 3.0 27.7 + - - -
48B PHE* 4.2 14.4 - - + +
49B THR 3.2 31.5 + - - +
50B HIS* 4.3 6.3 - - + +
63B PHE* 3.7 28.4 - - + -
65B ASN 3.4 8.6 + - - +
66B LYS* 3.2 31.6 + - - +
68B GLU* 1.3 79.5 - - - +
70B THR* 1.3 58.2 + - - +
72B PHE* 3.3 1.9 + - - +
73B LYS* 2.9 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 3.0 18.3 + - - +
67B GLN* 3.8 6.5 - - - +
69B ARG* 1.3 73.5 + - - +
71B LEU* 1.3 68.0 + - - +
73B LYS* 3.2 11.3 + - - +
74B GLU* 3.1 31.7 + - + +
135B LEU* 3.5 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN 3.1 12.3 + - - +
68B GLU* 3.3 8.5 + - - +
70B THR* 1.3 80.6 - - - +
72B PHE* 1.3 63.0 + - - +
74B GLU* 3.3 4.2 + - + +
75B LEU* 2.9 36.4 + - + +
90B LEU* 3.5 25.6 - - + -
95B ALA* 4.3 19.1 - - + +
98B PHE* 3.5 28.5 - - + -
99B VAL* 4.4 6.7 - - + -
128B MET* 3.8 6.5 - - + -
132B PHE* 3.6 38.4 - - + -
139B LEU* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 3.8 31.2 - + + -
52B VAL* 5.3 0.2 - - + -
61B TYR* 3.8 27.6 - + + -
63B PHE* 3.2 32.3 - + + -
68B GLU 2.9 14.3 + - - +
69B ARG 3.4 8.3 - - - +
71B LEU* 1.3 76.5 - - - +
73B LYS* 1.3 64.8 + - - +
75B LEU* 3.2 15.3 + - - +
76B ILE* 3.3 25.8 + - + +
83B PRO* 3.9 22.7 - - + -
86B ALA* 3.8 25.8 - - + -
87B LEU* 3.9 18.2 - - + -
90B LEU* 4.2 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.9 11.9 + - - -
49B THR 5.1 0.6 + - - -
50B HIS* 2.7 52.6 + - + +
69B ARG* 2.9 45.3 + - + +
70B THR* 3.2 9.4 + - - +
72B PHE* 1.3 76.4 - - - +
74B GLU* 1.3 65.9 + - - +
76B ILE* 3.3 21.5 - - - +
77B LYS* 3.6 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.1 23.9 + - + +
71B LEU* 3.7 8.3 - - + +
73B LYS* 1.3 76.6 - - - +
75B LEU* 1.3 67.1 + - - +
77B LYS* 3.2 42.6 + - - +
128B MET* 3.8 17.3 - - + -
131B ARG* 3.2 49.3 + - + +
132B PHE* 5.7 3.4 - - + -
135B LEU* 4.0 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 2.9 42.0 + - + +
72B PHE* 3.2 10.3 + - - +
74B GLU* 1.3 75.7 - - - +
76B ILE* 1.3 57.5 + - - +
77B LYS 3.2 0.5 + - - -
78B THR* 3.2 24.7 + - - +
81B VAL* 3.3 16.5 - - + +
86B ALA* 3.5 27.1 - - + +
89B ILE* 3.4 45.8 - - + -
90B LEU* 4.7 7.9 - - + -
98B PHE* 3.9 10.8 - - + -
124B LEU* 5.3 2.7 - - + -
128B MET* 3.3 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 4.2 17.5 - - + +
52B VAL* 5.2 3.6 - - + -
72B PHE* 3.6 30.7 - - + +
73B LYS* 3.3 17.7 - - - +
75B LEU* 1.3 73.0 - - - +
77B LYS* 1.3 60.4 + - + +
78B THR 3.3 2.8 + - - +
81B VAL 3.3 17.1 - - - +
82B GLY* 3.7 19.5 - - - -
83B PRO* 3.7 15.5 - - + -
86B ALA* 3.6 26.7 - - + -
----------------------------------------------------------
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