Contacts of the strand formed by residues 122 - 126 (chain A) in PDB entry 3MXW
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 LEU 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP 4.1 3.1 + - - +
84A ILE* 3.5 16.5 - - + -
85A ILE* 2.9 25.5 + - - +
106A LEU* 3.5 47.1 - - + +
109A LEU* 3.8 24.7 - - + -
110A ALA* 3.8 26.8 + - + +
113A VAL* 3.5 13.8 - - + +
121A LYS* 1.3 77.0 - - - +
123A ARG* 1.3 66.5 + - - +
148A ILE* 3.9 24.9 - - + -
149A THR 3.9 6.5 - - - +
161A LEU* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.3 29.7 - - + +
87A LYS* 3.5 27.7 - - - +
122A LEU* 1.3 75.4 - - - +
124A VAL* 1.3 69.3 + - - +
125A THR* 3.5 10.1 - - - +
148A ILE* 3.1 10.0 - - - +
149A THR* 2.9 60.0 + - - +
150A THR 3.8 13.2 - - - +
151A SER* 4.1 13.0 - - - +
153A ARG* 3.5 30.2 - - - +
31H ASP* 6.2 0.6 - - - +
97H GLU* 2.8 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.8 13.5 - - + -
85A ILE 2.7 8.7 + - - -
86A PHE* 3.6 37.9 - - + +
87A LYS* 2.9 28.6 + - - +
95A ASP* 3.9 7.5 - - + +
106A LEU* 3.9 18.2 - - + -
122A LEU* 4.9 0.7 - - + -
123A ARG* 1.3 78.0 - - - +
125A THR* 1.3 62.0 + - - +
126A GLU 3.3 31.4 - - - +
146A VAL* 4.2 7.9 - - + -
147A ASP 3.4 4.5 - - - +
148A ILE* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.9 12.8 - - + -
89A GLU* 3.4 5.5 - - - +
95A ASP* 3.0 4.3 - - - +
123A ARG* 3.5 30.5 - - - +
124A VAL* 1.3 73.6 - - - +
126A GLU* 1.3 60.4 + - - +
147A ASP* 2.8 27.4 + - - +
149A THR* 3.9 14.4 - - + +
180A HIS* 4.7 3.9 - - + +
401A CA 2.4 30.0 - - - -
97H GLU* 3.6 24.5 + - + +
98H ARG* 4.2 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.3 4.7 - - - +
90A GLU* 2.5 1.4 - - - +
95A ASP* 3.2 4.0 - - - +
124A VAL* 3.3 10.2 - - - +
125A THR* 1.3 81.8 + - - +
127A GLY* 1.3 60.3 + - - +
128A TRP 5.4 0.2 - - - -
129A ASP* 3.1 8.0 - - - +
133A HIS* 4.7 5.9 - - - +
134A HIS* 2.7 36.8 + - + +
140A HIS* 4.0 2.5 - - + +
146A VAL* 3.2 5.5 - - - -
147A ASP* 2.9 41.0 + - + +
401A CA 2.4 29.3 - - - -
402A CA 2.4 29.0 - - - -
98H ARG* 3.9 14.6 - - - +
----------------------------------------------------------
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