Contacts of the strand formed by residues 136 - 142 (chain A) in PDB entry 6S1M
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 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 4.2 23.5 - - - +
129A GLY 3.7 6.5 - - - -
130A VAL* 4.6 2.5 - - - -
134A GLY 4.1 0.6 + - - -
135A PHE* 1.3 73.7 - - - +
137A VAL* 1.3 60.9 + - - +
284A CYS* 3.8 13.1 - - - -
285A GLN* 3.1 40.8 + - - +
286A LEU* 3.1 9.5 + - - +
389A ASP* 4.2 13.5 + - - -
423A ARG* 4.6 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.2 21.3 - - + -
96A PHE* 4.1 29.1 - - + -
127A ALA 3.7 1.0 - - - +
128A PHE* 3.5 3.8 - - - +
129A GLY 2.9 37.7 + - - +
131A THR* 3.7 21.5 - - + -
135A PHE 4.4 1.3 - - - +
136A SER* 1.3 77.2 - - - +
138A CYS* 1.3 72.4 + - - +
139A CYS* 5.0 1.8 - - + -
284A CYS* 4.4 4.0 - - - -
286A LEU* 3.3 34.1 - - + +
288A ALA* 5.4 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 5.0 3.4 - - - -
127A ALA 3.6 4.7 - - - -
128A PHE* 4.0 24.0 - - + +
137A VAL* 1.3 79.4 - - - +
139A CYS* 1.3 66.0 + - - +
140A HIS* 3.8 27.8 - - - -
282A THR* 4.0 15.9 - - - +
284A CYS* 3.8 23.7 - - + +
286A LEU 2.9 9.2 + - - +
287A GLU* 3.4 9.1 - - + -
288A ALA 3.1 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.1 20.0 - - + -
125A LEU 3.6 1.0 - - - +
126A ARG* 3.5 5.5 - - - -
127A ALA* 2.9 43.8 + - + +
137A VAL* 5.0 1.1 - - + -
138A CYS* 1.3 77.1 - - - +
140A HIS* 1.3 64.4 + - - +
141A ILE* 4.0 17.5 + - - +
268A LEU* 4.3 19.7 - - - -
288A ALA* 4.0 6.1 - - + +
290A VAL* 3.8 27.8 - - - -
295A VAL* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 5.0 15.5 - + - -
124A VAL* 5.1 6.2 - - + +
125A LEU 3.5 3.7 + - - +
126A ARG* 4.2 30.7 - - + +
138A CYS* 3.8 15.6 - - - -
139A CYS* 1.3 72.0 - - - +
141A ILE* 1.3 59.4 + - - +
142A HIS* 3.9 8.8 + + + +
278A LYS* 4.2 20.5 - - + +
281A ALA* 6.0 2.0 - - + +
282A THR* 4.4 6.6 - - + +
287A GLU* 2.9 30.0 + - + -
288A ALA 3.3 16.9 + - - +
289A ASP* 3.5 17.6 - - - +
290A VAL* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.5 7.6 - - - +
125A LEU* 2.9 49.4 + - + +
127A ALA* 4.8 13.2 - - + -
139A CYS* 4.3 19.7 - - - +
140A HIS* 1.3 78.5 - - - +
142A HIS* 1.3 63.6 + - - +
144A PHE* 6.2 0.9 - - + -
254A PHE* 4.1 27.6 - - + -
266A LEU* 6.0 5.2 - - + -
290A VAL* 3.4 6.5 - - + +
291A LEU 4.5 1.1 - - - +
292A TRP* 3.6 33.7 - - + +
295A VAL* 4.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 5.3 8.3 - - - -
109A GLN* 6.0 0.6 - - - -
110A PRO* 4.8 21.0 - - + +
121A SER 5.6 0.9 + - - +
124A VAL* 3.4 33.1 - - + +
140A HIS* 3.7 11.5 - + + +
141A ILE* 1.3 78.7 - - - +
143A GLY* 1.3 59.8 + - - +
144A PHE* 3.8 2.2 - - - -
278A LYS* 6.4 0.7 - - + -
289A ASP* 2.4 35.5 + - - -
290A VAL 3.2 26.7 + - - +
291A LEU* 3.7 15.6 - - + +
292A TRP* 3.1 29.2 + - - +
----------------------------------------------------------
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