Contacts of the strand formed by residues 138 - 145 (chain H) in PDB entry 1S9C
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 CYS 138 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H GLY* 4.4 13.5 - - - -
64H ILE* 4.5 6.7 - - - -
94H LEU* 4.1 3.6 - - + -
95H GLU 3.2 12.6 - - - +
96H LEU* 3.9 17.5 - - + -
97H TYR* 4.0 4.7 - - - -
100H LEU* 4.7 4.3 - - - -
128H VAL 3.8 0.6 - - - +
129H TYR* 3.5 4.7 - - - -
130H SER* 3.1 49.0 + - - -
136H LEU* 3.7 3.7 - - - +
137H ILE* 1.3 89.0 - - + +
139H HIS* 1.3 61.5 + - - +
140H ASN* 4.2 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H TYR* 3.6 26.5 - + - +
94H LEU* 3.3 6.1 - - - +
95H GLU* 3.0 32.8 + - + +
97H TYR* 3.7 27.7 + - + +
127H ASP* 2.5 32.6 + - + -
128H VAL 3.7 3.6 - - - -
129H TYR* 3.7 34.5 + + + -
138H CYS* 1.3 76.0 - - - +
140H ASN* 1.3 87.7 + - - +
141H GLN* 4.5 3.6 - - + -
162H LYS* 4.5 16.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H GLY 3.0 21.9 + - - -
62H VAL* 3.3 17.1 - - - +
65H GLY* 3.7 14.8 - - - +
92H GLN* 3.2 18.1 + - - +
93H TYR 3.2 2.4 - - - +
94H LEU* 3.5 16.6 - - - +
126H MET 3.4 0.7 - - - +
127H ASP* 3.2 6.4 - - - -
128H VAL* 3.1 34.7 + - + -
138H CYS* 4.2 7.5 - - - -
139H HIS* 1.3 80.9 - - - +
141H GLN* 1.3 60.8 + - - +
142H PHE* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLU* 4.1 0.9 - - - +
92H GLN* 3.6 4.5 + - - +
93H TYR* 2.8 43.4 + - + +
125H ILE* 3.4 27.4 - - + +
126H MET 3.7 1.1 - - - -
127H ASP* 3.0 22.3 + - - +
139H HIS* 4.1 5.2 - - - +
140H ASN* 1.3 72.5 - - - +
142H PHE* 1.3 63.4 + - - +
143H SER* 3.6 6.8 + - - -
160H LYS 2.6 29.7 + - - -
161H VAL* 3.4 12.0 - - - +
162H LYS* 3.2 36.5 + - - +
243H LYS* 4.6 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H VAL* 3.7 12.1 - - + -
65H GLY 3.5 3.8 - - - -
66H GLN* 3.4 43.1 - - + -
89H HIS* 4.0 13.5 - + - +
91H GLU 4.2 0.2 - - - -
92H GLN* 3.3 27.4 - - - -
124H ILE 3.3 5.7 - - - +
125H ILE* 3.5 1.9 - - - -
126H MET* 3.0 46.2 + - + +
128H VAL* 3.4 15.0 - - + -
140H ASN* 3.4 27.4 - - + -
141H GLN* 1.3 71.2 - - - +
143H SER* 1.3 60.3 + - - +
144H LEU* 3.7 20.8 - - + +
217H LEU* 4.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H HIS* 3.5 4.4 + - - -
90H GLY* 2.7 34.8 + - - -
91H GLU* 3.1 48.6 + - - +
123H VAL* 3.9 19.1 - - - +
124H ILE 4.0 4.7 - - - -
125H ILE* 4.7 6.1 - - - +
141H GLN* 3.6 6.8 + - - -
142H PHE* 1.3 72.0 - - - +
144H LEU* 1.3 55.1 + - - +
243H LYS* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H VAL* 3.3 27.6 - - + -
88H LEU 3.3 4.3 - - - +
89H HIS* 4.5 13.5 - - + +
90H GLY* 5.6 0.2 - - - -
123H VAL* 3.2 6.5 - - - +
124H ILE* 2.9 59.1 + - + +
126H MET* 4.2 24.5 - - - -
142H PHE* 3.7 25.8 - - + +
143H SER* 1.3 80.6 - - - +
145H PHE* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H VAL* 3.2 10.3 - - - +
88H LEU* 2.6 55.9 + - + +
90H GLY* 5.0 8.7 - - - +
118H LYS* 4.6 14.1 - - + -
120H SER* 4.2 9.2 - - - -
121H GLY* 3.4 24.0 - - - -
122H VAL 3.8 20.9 - - - -
123H VAL* 4.4 12.3 - - + -
124H ILE* 5.4 0.7 - - - -
144H LEU* 1.3 76.2 - - - +
146H LEU* 1.3 83.0 + - - +
----------------------------------------------------------
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