Contacts of the helix formed by residues 131 - 140 (chain B) in PDB entry 5M4G
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 GLU 131 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.1 20.4 + - - +
114B LYS* 4.8 4.3 + - - -
127B GLN* 4.4 14.3 - - - +
128B TYR* 3.0 28.3 + - - +
130B ASP* 1.3 93.2 - - - +
132B ILE* 1.3 63.9 + - - +
133B ALA 3.3 2.7 - - - -
134B SER* 3.3 13.8 + - - +
135B VAL* 3.0 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 5.0 2.0 - - + -
83B TYR* 4.0 37.9 - - + -
85B VAL* 4.7 5.8 - - + -
96B PHE* 3.6 33.7 - - + -
128B TYR 3.9 1.2 + - - -
129B VAL* 3.1 19.9 + - + +
130B ASP 3.4 1.7 - - - -
131B GLU* 1.3 77.3 - - - +
133B ALA* 1.3 66.5 + - + +
136B LEU* 2.9 42.1 + - + +
163B PHE* 3.6 39.9 - - + -
164B ASP 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP 5.0 1.0 + - - -
131B GLU 3.3 0.6 - - - -
132B ILE* 1.3 81.4 - - + +
134B SER* 1.3 54.1 + - - +
136B LEU 3.9 0.2 - - - -
137B THR* 2.7 39.3 + - - +
163B PHE* 4.1 15.0 - - + -
164B ASP 3.7 22.4 - - - +
165B GLY* 4.7 5.6 - - - -
169B PHE* 3.9 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU* 3.3 17.8 + - - -
133B ALA* 1.3 79.6 - - - +
135B VAL* 1.3 65.6 + - - +
137B THR* 3.2 7.5 + - - -
138B SER* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 5.1 1.8 - - + -
96B PHE* 3.8 23.1 - - + -
125B ASP* 5.5 1.3 - - - +
127B GLN* 3.8 36.3 - - + +
131B GLU* 3.0 30.9 + - + +
132B ILE 3.9 2.5 - - - +
134B SER* 1.3 76.7 - - - +
136B LEU* 1.3 61.5 + - + +
138B SER* 2.6 24.3 + - - +
139B GLN* 3.3 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.4 14.6 - - + -
47B VAL* 4.6 7.4 - - + -
85B VAL* 4.3 22.2 - - + -
96B PHE* 4.7 6.5 - - + -
132B ILE* 2.9 32.8 + - + +
135B VAL* 1.3 76.2 - - + +
137B THR* 1.3 62.6 + - - +
139B GLN* 3.1 24.5 + - - +
141B PRO* 2.9 27.9 - - + +
144B LEU* 4.4 16.6 - - + -
163B PHE* 3.7 30.7 - - + -
169B PHE* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ALA* 2.7 28.4 + - - +
134B SER* 3.2 8.3 + - - -
136B LEU* 1.3 73.8 - - - +
138B SER* 1.3 64.2 + - - +
140B LYS* 3.1 28.7 + - + +
141B PRO* 5.0 0.4 - - - -
169B PHE* 3.6 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 3.0 12.0 + - - -
135B VAL* 2.6 27.2 + - - +
137B THR* 1.3 78.0 - - - +
139B GLN* 1.3 62.7 + - - +
140B LYS* 3.2 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.5 24.5 - - + +
85B VAL* 5.1 4.6 - - - +
87B ASP* 6.1 0.2 - - - +
92B LYS* 4.2 22.0 - - - +
94B THR* 4.6 10.3 + - - -
125B ASP* 5.6 1.8 + - - -
135B VAL* 3.3 32.8 + - - +
136B LEU* 3.1 18.5 + - - +
138B SER* 1.3 78.5 + - - +
140B LYS* 1.3 72.4 + - - +
141B PRO* 3.4 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 5.7 1.2 - - - -
137B THR* 3.1 22.6 + - + +
138B SER* 4.2 6.1 - - - +
139B GLN* 1.3 82.8 - - - +
141B PRO* 1.3 76.5 + - - +
142B SER 3.7 0.9 + - - -
----------------------------------------------------------
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