Contacts of the strand formed by residues 121 - 129 (chain A) in PDB entry 7MHN
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 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS* 3.2 3.9 - - - -
118A TYR* 2.8 38.2 + - - +
119A ASN 3.2 3.8 + - - -
120A GLY* 1.3 77.5 - - - +
122A PRO* 1.3 74.5 - - - +
123A SER* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 4.4 27.8 - - + +
17A MET* 6.0 1.8 - - + -
115A LEU* 4.0 21.8 - - + -
116A ALA 3.8 0.4 - - - +
117A CYS* 3.6 14.6 - - - -
120A GLY 4.5 2.2 - - - +
121A SER* 1.3 89.1 - - - +
123A SER* 1.3 60.3 + - - +
124A GLY 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 2.7 20.7 + - - +
118A TYR* 3.6 32.0 - - - -
121A SER 3.5 0.8 + - - -
122A PRO* 1.3 76.6 - - - +
124A GLY* 1.3 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.5 9.2 - - - +
116A ALA* 3.0 29.0 + - - +
122A PRO* 3.8 1.2 - - - +
123A SER* 1.3 80.1 - - - +
125A VAL* 1.3 67.5 + - - +
126A TYR* 5.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.3 27.5 - - + +
8A PHE 4.2 10.5 - - - +
10A SER* 4.0 22.9 - - - +
113A SER* 4.3 8.1 - - - -
114A VAL 3.1 13.2 - - - +
115A LEU* 4.5 8.7 - - + -
124A GLY* 1.3 77.6 - - - +
126A TYR* 1.3 68.7 + - - +
150A PHE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.1 7.6 - - - -
113A SER* 3.3 2.1 - - - -
114A VAL* 2.9 56.7 + - + +
116A ALA* 4.3 11.7 - - + -
124A GLY 5.1 0.4 - - - -
125A VAL* 1.3 81.8 - - - +
127A GLN* 1.3 62.1 + - - +
128A CYS* 4.0 16.2 + - + -
137A LYS 5.1 1.1 - - - -
138A GLY* 3.7 14.3 - - - -
139A SER* 3.0 42.6 + - - -
140A PHE* 3.4 24.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.8 34.9 - - + +
6A MET 3.3 33.2 + - - +
7A ALA* 3.7 1.4 - - - +
8A PHE* 4.2 17.4 - - - -
111A THR* 3.9 22.9 + - - -
112A PHE* 3.2 15.1 - - - +
113A SER* 2.8 26.0 + - - -
126A TYR* 1.3 75.1 - - - +
128A CYS* 1.3 61.5 + - - +
290A GLU* 4.0 12.2 - - - +
291A PHE* 6.1 2.9 - - + -
295A ASP* 4.1 12.9 + - - -
401A DMS 5.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 3.4 8.4 - - - -
112A PHE* 3.0 59.8 + - - +
114A VAL* 3.9 20.9 - - - -
126A TYR* 4.0 15.2 + - + -
127A GLN* 1.3 75.0 - - - +
129A ALA* 1.3 65.3 + - - +
136A ILE* 4.1 12.3 - - + -
137A LYS 4.6 11.7 - - - +
290A GLU* 4.2 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY 4.9 1.8 - - - +
110A GLN 3.9 7.0 - - - +
111A THR* 4.2 13.5 - - + -
112A PHE* 4.2 1.8 - - - -
128A CYS* 1.3 77.8 - - - +
130A MET* 1.3 60.4 + - - +
131A ARG* 3.7 19.9 + - - +
136A ILE* 3.3 24.5 - - - +
137A LYS 4.8 1.0 + - - -
200A ILE* 4.3 11.7 - - + -
289A ASP 4.5 0.4 - - - +
290A GLU* 3.7 30.6 + - + +
----------------------------------------------------------
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