Contacts of the helix formed by residues 74 - 86 (chain B) in PDB entry 1SA4
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 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.6 34.9 + - - +
73B LEU* 1.3 66.7 - - - +
75B ARG* 1.3 64.1 + - - +
76B GLU 3.4 2.7 - - - -
77B LYS* 3.1 47.8 + - + +
78B HIS* 3.0 30.4 + - + +
344B GLN* 2.7 26.9 - - + +
345B CYS 5.6 2.0 - - - +
346B PRO* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 2.8 30.1 + - + +
74B GLN* 1.3 69.8 - - - +
76B GLU* 1.3 69.2 + - + +
78B HIS* 3.2 9.7 + - - +
79B PHE* 2.8 28.9 + - - +
114B LEU* 3.1 49.3 + - + +
115B ASP* 5.2 2.4 - - - +
116B GLU* 4.7 5.2 + - - +
391B GLU* 2.5 35.3 + - - +
392B ASN* 4.1 2.0 + - - +
393B ALA 2.7 31.5 + - - -
394B LEU* 4.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLN 3.4 0.8 - - - -
75B ARG* 1.3 85.9 - - + +
77B LYS* 1.3 64.9 + - + +
79B PHE* 3.3 14.9 + - - +
80B HIS* 2.9 43.8 + - + +
116B GLU* 3.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLN* 3.1 47.1 + - + +
76B GLU* 1.3 77.7 - - + +
78B HIS* 1.3 63.8 + - - +
80B HIS* 3.4 7.9 + - - +
81B TYR* 3.2 18.2 + - - +
345B CYS 4.8 0.2 - - - +
346B PRO* 2.9 37.8 + - - +
347B ALA 4.3 5.1 - - - +
348B GLY* 3.6 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.0 14.3 - - + +
74B GLN* 3.0 28.0 + - + -
75B ARG* 3.6 6.5 - - - +
77B LYS* 1.3 77.0 - - - +
79B PHE* 1.3 62.2 + - - +
81B TYR* 3.3 2.6 + - - +
82B LEU* 3.0 34.0 + - + +
114B LEU* 4.0 15.0 - - + -
344B GLN* 2.9 34.9 + - + -
345B CYS 4.4 3.4 - - - -
348B GLY* 3.7 4.7 - - - -
349B GLY* 2.7 49.4 + - - +
350B LEU* 3.5 21.3 - - + +
363B THR* 5.5 0.7 - - + -
367B LEU* 5.0 3.8 - - + -
----------------------------------------------------------
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 ARG 2.8 17.8 + - - +
76B GLU* 3.5 17.0 - - - +
78B HIS* 1.3 76.5 - - - +
80B HIS* 1.3 81.6 + + - +
82B LEU* 3.3 7.9 + - - +
83B LYS* 2.8 53.9 + - + +
111B LEU* 3.7 17.7 - - + -
114B LEU* 4.4 2.2 - - + +
116B GLU* 3.5 47.3 - - + +
117B PRO 5.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.9 42.4 + - + +
77B LYS* 3.4 6.7 + - - +
79B PHE* 1.3 97.0 - + - +
81B TYR* 1.3 62.1 + - - +
83B LYS* 3.9 13.2 - - + +
84B ARG* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS 3.2 13.7 + - - +
78B HIS 3.5 8.3 - - - +
80B HIS* 1.3 76.6 - - - +
82B LEU* 1.3 69.5 + - + +
84B ARG* 3.5 5.0 + - + +
85B GLY 3.1 17.3 + - - -
93B TYR* 4.0 3.5 + - - -
347B ALA 4.8 0.9 - - - +
348B GLY* 4.1 7.2 - - - -
349B GLY* 3.4 20.2 - - - -
358B ARG* 3.4 46.8 + - + +
359B ASP* 3.3 32.1 + - - -
360B PHE* 3.4 38.5 + + - -
363B THR* 3.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 3.0 25.2 + - + +
79B PHE 3.7 2.9 - - - +
81B TYR* 1.3 75.7 - - + +
83B LYS* 1.3 67.1 + - - +
85B GLY* 3.1 1.9 + - - -
86B LEU* 3.1 19.8 + - - +
106B TRP 4.8 0.4 - - - +
107B ILE* 3.6 27.1 - - + +
110B SER* 3.6 36.1 - - - +
111B LEU* 3.9 22.9 - - + -
114B LEU* 3.7 22.9 - - + -
360B PHE* 4.1 18.2 - - + +
363B THR* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 2.8 52.2 + - + +
80B HIS* 3.9 13.2 + - - +
82B LEU* 1.3 74.2 - - - +
84B ARG* 1.3 64.4 + - - +
86B LEU* 3.6 16.2 + - - +
87B ARG* 4.0 7.8 + - - +
111B LEU* 4.8 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS 3.2 15.6 + - - +
81B TYR* 3.7 5.6 - - - +
82B LEU 3.2 0.6 - - - -
83B LYS* 1.3 80.4 - - - +
85B GLY* 1.3 62.7 + - - +
87B ARG* 3.2 18.5 + - - +
88B GLN* 3.2 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.8 8.3 - - - +
81B TYR 3.1 11.1 + - - -
82B LEU 3.1 1.9 + - - -
84B ARG* 1.3 73.2 - - - +
86B LEU* 1.3 61.0 + - - +
87B ARG 3.0 6.3 + - - -
88B GLN 3.8 1.6 - - - +
89B LEU* 3.6 27.7 - - - +
107B ILE* 3.5 11.7 - - - +
360B PHE* 3.6 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.4 13.1 - - + +
88A VAL* 2.9 29.0 + - + -
82B LEU 3.1 15.7 + - - +
83B LYS* 3.8 9.2 - - - +
84B ARG 3.3 0.4 - - - -
85B GLY* 1.3 77.0 - - - +
87B ARG* 1.3 59.8 + - - +
104B CYS* 4.7 6.1 - - - -
107B ILE* 3.6 21.9 - - + +
108B LEU* 4.2 23.3 - - + -
111B LEU* 4.3 14.1 - - + -
118B ILE* 5.4 0.7 - - + -
122B VAL* 3.3 33.9 - - + -
126B VAL* 4.4 17.3 - - + -
----------------------------------------------------------
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