Contacts of the strand formed by residues 141 - 150 (chain B) in PDB entry 1MNG
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 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN* 2.9 20.1 + - - -
137B LYS* 4.9 17.2 - - - +
138B ASP* 3.1 8.7 + - - -
139B PRO 3.4 2.6 + - - -
140B PHE* 1.3 78.3 - - - +
142B LYS* 1.3 62.9 + - - +
143B LEU* 5.0 1.6 - - - +
200B PHE* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN* 3.6 13.0 + - - +
137B LYS* 3.5 3.5 - - - -
138B ASP* 3.0 45.9 + - - +
140B PHE* 3.8 14.8 - - + +
141B GLY* 1.3 83.7 - - - +
143B LEU* 1.3 62.7 + - - +
144B HIS* 3.5 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.3 4.5 - - + -
105B ALA* 3.8 30.3 - - + +
106B ILE* 4.0 16.6 - - + -
109B GLN* 2.8 26.0 + - - +
110B PHE* 3.6 35.6 - - + -
135B LEU* 4.2 6.7 - - + -
136B VAL 3.3 12.8 - - - +
137B LYS* 4.3 7.6 - - + -
141B GLY 5.3 0.7 - - - +
142B LYS* 1.3 76.8 - - - +
144B HIS* 1.3 65.8 + - - +
162B ILE* 4.0 21.5 - - + -
200B PHE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.7 1.6 - - - -
134B TRP 3.8 0.2 - - - +
135B LEU* 3.5 6.8 - - - +
136B VAL* 2.9 44.1 + - + +
138B ASP* 2.7 28.3 + - - +
142B LYS* 3.5 19.5 - - + +
143B LEU* 1.3 80.1 + - - +
145B VAL* 1.3 64.3 + - - +
146B LEU* 4.0 9.2 - - + -
159B PHE* 3.6 28.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.0 18.0 - - + -
116B LEU* 3.9 28.0 - - + -
119B LYS* 3.7 38.6 - - + +
120B LEU* 3.8 11.4 - - + -
123B ALA* 3.7 15.8 - - + +
134B TRP 3.4 10.1 - - - +
135B LEU* 4.4 2.9 - - + -
144B HIS* 1.3 75.2 - - - +
146B LEU* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 4.4 8.3 - - - +
133B ALA* 3.6 2.9 - - - +
134B TRP* 2.8 51.7 + - + +
136B VAL* 3.8 26.7 - - + -
144B HIS* 4.4 6.5 - - + +
145B VAL* 1.3 76.4 - - - +
147B SER* 1.3 70.1 + - - +
148B THR* 4.0 9.9 - - + -
154B PRO* 4.3 9.4 - - + -
157B GLU* 5.6 1.8 - - - +
159B PHE* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.8 24.2 + - - +
126B GLY 5.4 0.5 - - - -
127B ARG* 2.8 41.8 + - - +
132B TRP 3.3 14.1 - - - -
133B ALA* 4.3 2.0 - - - -
134B TRP* 4.4 0.2 - - - -
146B LEU* 1.3 79.9 - - - +
148B THR* 1.3 67.5 + - - +
149B PRO* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 3.5 7.9 + - - -
131B GLY* 3.1 3.8 - - - -
132B TRP* 3.0 31.1 + - - +
134B TRP* 2.8 29.1 + - + +
146B LEU* 4.0 10.3 - - + -
147B SER* 1.3 78.8 - - - +
149B PRO* 1.3 70.5 + - + +
152B ASP* 2.8 33.5 + - + +
153B ASN 4.7 0.4 - - - -
154B PRO* 4.2 13.5 - - + -
157B GLU* 6.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 5.3 2.5 - - - +
127B ARG* 3.5 27.6 - - - +
130B SER 3.6 5.4 - - - +
147B SER 4.7 0.4 - - - +
148B THR* 1.3 87.8 - - + +
150B ASN* 1.3 79.6 + - - +
151B GLN 3.3 0.2 + - - -
152B ASP* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.9 30.1 + - + +
129A GLY* 3.5 23.4 - - - -
130A SER 4.3 2.8 + - - +
150A ASN* 5.3 5.1 - - - +
75B ASN* 5.2 2.0 - - - +
130B SER* 2.9 24.8 + - - +
131B GLY* 3.6 0.9 - - - -
132B TRP* 3.3 15.2 - - - -
149B PRO* 1.3 81.8 - - - +
151B GLN* 1.3 59.7 + - - +
152B ASP* 5.0 3.1 - - - +
168B TRP* 2.9 30.8 + - + +
----------------------------------------------------------
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