Contacts of the helix formed by residues 65 - 77 (chain B) in PDB entry 1S5E
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 SER 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.3 14.7 - - - +
63B SER* 3.3 2.3 - - - -
64B ILE* 1.3 85.7 - - - +
66B LEU* 1.3 63.1 + - - +
67B ARG* 3.6 20.8 + - - +
68B SER* 3.0 29.8 + - - -
69B ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.4 31.2 - - + -
65B SER* 1.3 72.7 - - - +
67B ARG* 1.3 64.9 + - - +
69B ALA* 3.2 1.0 + - - -
70B HIS* 2.8 29.7 + - + +
85B ILE* 3.6 37.5 - - + -
128B TYR* 3.8 37.5 - - + +
135B LEU* 5.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 3.2 17.4 + - - +
66B LEU* 1.3 80.0 - - - +
68B SER* 1.3 64.2 + - - +
70B HIS* 3.4 5.8 + - - +
71B LEU* 3.0 37.1 + - + +
14E ASN* 5.9 3.9 - - - +
89E ASN* 5.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 3.9 16.2 - - - -
64B ILE* 5.0 4.2 - - - +
65B SER* 3.0 26.2 + - - -
67B ARG* 1.3 79.6 + - - +
69B ALA* 1.3 64.8 + - - +
71B LEU* 3.2 9.6 + - - +
72B VAL* 3.0 27.8 + - - +
110B GLU 5.7 4.0 - - - -
111B GLN* 5.1 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.4 46.7 - - + +
7B ARG* 4.1 6.1 - - - +
8B ALA* 3.8 8.2 - - - +
63B SER* 3.6 10.0 + - - +
65B SER 3.1 7.5 + - - +
66B LEU 3.8 2.9 - - - +
68B SER* 1.3 77.1 - - - +
70B HIS* 1.3 57.6 + - - +
72B VAL* 3.3 4.5 + - - +
73B GLY* 2.8 26.5 + - - -
85B ILE* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 2.8 21.0 + - + +
67B ARG* 3.7 6.9 - - - +
69B ALA* 1.3 73.8 - - - +
71B LEU* 1.3 61.3 + - - +
73B GLY* 3.2 1.4 + - - -
74B GLN* 2.9 61.1 + - + +
83B TYR* 4.4 7.4 - - - -
85B ILE* 3.6 24.0 - - + +
130B VAL* 4.7 2.8 - - + +
133B GLY 3.4 13.2 + - - -
134B VAL* 5.4 0.2 - - - -
135B LEU* 3.9 27.8 + - + +
90E ASN* 4.1 23.4 + - - +
----------------------------------------------------------
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 ARG* 3.0 31.1 + - + +
68B SER* 3.5 10.5 - - - +
70B HIS* 1.3 77.4 - - - +
72B VAL* 1.3 60.4 + - + +
74B GLN* 3.3 15.9 + - + +
75B THR* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 4.6 8.7 - - - +
53B VAL* 3.8 32.5 - - + -
63B SER* 4.4 9.9 - - - +
68B SER* 3.0 21.0 + - - +
69B ALA* 3.6 8.5 - - - +
71B LEU* 1.3 76.4 - - + +
73B GLY* 1.3 63.0 + - - +
75B THR* 2.7 23.7 + - - +
76B ILE* 2.9 19.4 + - + +
110B GLU* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.6 25.3 - - - +
53B VAL* 5.1 0.4 - - - -
69B ALA 2.8 10.7 + - - -
70B HIS 3.2 4.2 + - - -
72B VAL* 1.3 77.9 - - - +
74B GLN* 1.3 56.8 + - - +
76B ILE* 5.0 0.4 - - - -
77B LEU* 2.8 41.8 + - - +
83B TYR* 3.4 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 2.9 50.7 + - + +
71B LEU* 3.6 19.9 - - + +
72B VAL 3.2 0.2 - - - -
73B GLY* 1.3 73.3 - - - +
75B THR* 1.3 63.4 + - + +
78B SER* 3.4 24.8 + - - +
83B TYR* 3.5 13.0 + - - +
133B GLY* 3.4 18.4 + - - +
90E ASN 6.1 0.2 - - - -
91E LYS* 5.4 0.2 - - - +
92E THR* 3.2 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 2.9 28.0 - - + +
72B VAL* 2.7 22.2 + - - +
74B GLN* 1.3 81.0 - - + +
76B ILE* 1.3 74.3 + - - +
78B SER* 4.6 5.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
49B GLN* 3.7 40.4 - - + +
51B GLY* 3.8 20.4 + - - +
52B PHE* 3.4 42.2 - - - +
53B VAL* 3.8 6.1 - - + +
72B VAL* 2.9 29.2 + - + +
75B THR* 1.3 93.7 - - - +
77B LEU* 1.3 65.8 + - + +
78B SER* 3.5 6.1 + - - +
80B HIS* 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.7 42.8 - - + +
9B ASP* 3.8 10.5 - - - +
10B SER* 4.1 9.6 - - - +
51B GLY 3.6 26.5 - - - +
52B PHE* 4.5 5.2 - - - -
53B VAL* 4.5 4.0 - - + +
73B GLY* 2.8 18.7 + - - +
76B ILE* 1.3 83.1 - - + +
78B SER* 1.3 65.6 + - - +
80B HIS* 3.1 39.2 + - + +
83B TYR* 3.7 28.5 - - + -
----------------------------------------------------------
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