Contacts of the helix formed by residues 102 - 108 (chain C) in PDB entry 1SA0
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 102 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA 3.7 2.7 + - - +
100C ALA* 4.1 5.0 - - - +
101C ASN* 1.3 82.3 - - - +
103C TYR* 1.3 54.6 + - - +
104C ALA* 2.9 21.8 - - - +
105C ARG* 2.4 57.5 + - - +
106C GLY 3.5 1.2 + - - -
144C GLY* 4.1 5.4 - - - -
182C VAL* 5.0 0.4 - - + -
186C ASN* 3.6 2.0 - - - -
407C TRP* 3.4 27.4 + - - -
408C TYR* 3.6 24.8 - - + +
411C GLU* 4.0 5.2 + - - +
257D VAL* 4.7 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASN* 1.3 67.2 - - - +
104C ALA* 1.3 58.6 + - - +
105C ARG 2.7 13.2 + - - -
106C GLY 2.8 1.7 + - - -
107C HIS* 2.8 57.2 + + + +
108C TYR* 4.4 0.9 - + - -
144C GLY 4.2 4.4 + - - -
147C SER* 3.7 10.3 - - - +
148C GLY* 3.7 23.6 - - - +
151C SER* 3.5 19.1 + - - -
186C ASN* 2.7 24.3 + - - +
189C LEU* 3.9 31.6 - - + -
190C THR* 3.7 31.9 - - - -
193C THR* 2.9 20.8 + - - +
408C TYR* 3.9 0.2 - - - -
413C MET* 4.1 9.4 - - - -
417C GLU* 3.8 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASN* 2.7 23.3 + - - +
103C TYR* 1.3 80.8 - - - +
105C ARG* 1.3 58.1 + - - +
108C TYR* 3.2 36.8 - - + +
109C THR 3.8 1.2 + - - -
408C TYR* 3.5 30.7 - - + +
411C GLU* 3.9 11.8 - - + +
413C MET* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU* 3.5 20.6 + - - -
98C ASP 3.2 21.4 + - - -
99C ALA 3.2 15.7 - - - +
100C ALA* 3.0 24.3 - - - +
102C ASN* 2.4 24.2 + - - +
103C TYR 2.7 0.2 + - - -
104C ALA* 1.3 72.2 - - - +
106C GLY* 1.3 65.0 + - - +
107C HIS 3.3 0.5 + - - -
108C TYR 3.4 0.2 + - - -
109C THR* 3.3 19.7 + - - +
110C ILE* 3.0 49.7 + - + +
411C GLU* 2.8 35.0 + - - +
2D ARG* 4.0 7.1 - - - +
164D ARG* 4.5 0.4 - - - +
253D ARG* 2.6 39.9 - - - +
112E ARG* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 4.7 2.5 - - - -
99C ALA* 4.4 2.9 + - - -
102C ASN 3.5 3.6 + - - -
103C TYR 2.8 5.7 + - - -
105C ARG* 1.3 79.8 - - - +
107C HIS* 1.3 54.3 + - - -
110C ILE* 4.2 10.9 - - - +
111C GLY* 3.3 22.9 - - - -
144C GLY 4.5 7.2 + - - -
145C THR* 4.7 5.8 - - - -
148C GLY* 4.0 2.9 - - - -
149C PHE* 3.5 29.3 + - - +
152C LEU* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 2.8 52.6 + - + +
106C GLY* 1.3 73.5 - - - -
108C TYR* 1.3 98.3 + + + +
111C GLY* 5.1 0.2 - - - -
148C GLY* 3.6 12.1 + - - +
151C SER* 3.9 2.2 - - - -
152C LEU* 3.4 60.9 + - + +
155C GLU* 3.1 28.5 + - - -
193C THR* 4.9 2.2 - - - +
417C GLU* 5.2 0.4 + - - -
101E LEU* 5.3 1.2 - - - +
104E LYS* 5.9 3.6 - - - +
105E MET* 4.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 4.4 2.9 - + - -
104C ALA* 3.2 25.9 + - + +
105C ARG 3.4 3.7 + - - -
107C HIS* 1.3 107.1 + + - +
109C THR* 1.3 73.7 + - - +
112C LYS* 3.2 27.5 + - - +
411C GLU* 5.2 1.3 - - + +
412C GLY 5.4 0.4 - - - -
413C MET* 3.5 31.2 - - + -
417C GLU* 2.5 35.2 + - - -
104E LYS* 4.2 22.5 - - + +
105E MET* 4.3 16.8 - - + -
108E ASN* 3.0 44.2 - - + +
----------------------------------------------------------
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