Contacts of the strand formed by residues 130 - 137 (chain F) in PDB entry 1MA1
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 GLY 130 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ALA* 5.0 3.6 - - - -
128F GLY 3.6 3.0 + - - -
129F SER* 1.3 76.2 - - - +
131F TRP* 1.3 67.4 + - - -
148F VAL 2.9 13.0 - - - -
149F GLU* 4.1 0.2 - - - -
150F LYS 3.6 11.2 - - - -
167F VAL* 2.9 35.2 + - - +
168F TRP* 3.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F LEU* 3.5 43.2 - - + +
80F HIS* 3.6 35.0 - + - -
83F PHE* 3.8 4.7 - - + -
122F ALA 5.2 1.8 - - - -
126F ALA* 5.1 1.4 - - - +
130F GLY* 1.3 74.1 - - - -
132F ALA* 1.3 60.3 + - - +
133F VAL* 4.0 15.9 - - + -
147F GLN* 3.5 9.0 - - - +
148F VAL* 2.7 38.5 + - + +
150F LYS 3.0 20.9 + - - -
151F HIS* 2.9 23.9 + + - -
164F VAL* 3.4 31.4 - - + -
165F LEU 3.4 5.8 - - - -
166F ASP* 3.3 49.6 - - + -
167F VAL* 4.1 4.0 - - - +
168F TRP* 3.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F PHE* 3.3 33.7 - - + +
122F ALA* 4.0 9.9 - - + -
123F ALA* 3.9 31.3 - - + +
131F TRP* 1.3 71.9 - - - +
133F VAL* 1.3 63.5 + - - +
145F ILE* 5.0 0.2 - - + -
146F MET 3.7 4.3 - - - +
165F LEU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PRO* 6.1 2.7 - - + -
79F LEU* 4.2 6.5 - - + -
119F PHE* 3.8 4.6 - - - -
131F TRP* 4.0 17.0 - - + -
132F ALA* 1.3 80.7 - - - +
134F LEU* 1.3 73.1 + - - +
135F THR* 5.0 2.9 - - - -
145F ILE* 3.4 4.5 - - - -
146F MET* 2.9 51.3 + - + +
148F VAL* 4.0 16.8 - - + -
161F ILE* 4.2 17.0 - - + -
163F LEU 3.2 10.5 - - - +
164F VAL* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 4.5 14.6 - - + -
105F ILE* 5.2 3.4 - - + -
109F PHE* 4.6 1.8 - - + -
115F PHE* 4.0 31.9 - - + -
119F PHE* 3.7 8.7 - - + -
133F VAL* 1.3 75.9 - - - +
135F THR* 1.3 70.1 + - - +
143F LEU* 4.2 21.3 - - + -
144F PHE 3.3 21.5 - - - +
145F ILE* 4.1 7.4 - - + +
162F LEU* 2.9 44.6 + - + -
163F LEU* 2.8 31.2 + - + +
193F TRP* 5.6 1.1 - - + -
196F VAL* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F VAL* 5.0 2.7 - - - -
134F LEU* 1.3 75.1 - - - +
136F TYR* 1.3 67.5 + - - +
143F LEU* 3.3 13.0 - - - +
144F PHE* 2.8 46.7 + - + +
146F MET* 3.7 35.4 - - + -
159F PHE* 3.4 12.4 - - + +
160F ARG 2.6 37.0 + - - -
162F LEU* 4.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F TYR* 3.9 12.3 + + - -
135F THR* 1.3 85.6 + - - +
137F CYS* 1.3 58.5 + - - +
138F GLN* 3.2 49.0 + - + +
141F ASP* 2.5 50.3 + - - +
142F ARG 3.4 16.8 - - - -
143F LEU* 4.2 4.0 - - + -
144F PHE 4.4 0.4 - - - +
159F PHE* 3.6 15.9 - - - +
160F ARG 4.4 2.9 + - - -
162F LEU* 4.2 8.3 - - + -
200F PHE* 4.0 15.0 - + + -
203F ILE* 3.9 48.5 - - + +
204F LEU 4.5 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.0 25.4 - - - -
136F TYR* 1.3 72.6 - - - +
138F GLN* 1.3 56.3 + - - +
139F ARG* 3.2 17.2 + - - -
140F THR* 3.3 29.4 - - - +
141F ASP* 2.5 37.6 + - - -
142F ARG 2.8 11.0 + - - +
144F PHE* 3.6 22.1 - - + -
159F PHE* 3.6 15.2 - - + -
----------------------------------------------------------
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