Contacts of the helix formed by residues 137 - 144 (chain B) in PDB entry 2G27
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 PRO 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.9 24.5 - - - +
101B GLN* 4.0 0.7 - - - +
124B GLY 4.8 4.5 - - - +
125B MET 5.8 0.2 - - - -
126B GLY 3.6 17.0 - - - +
127B PHE 4.0 0.4 - - - -
128B ILE* 3.2 48.2 - - + +
135B VAL 3.4 2.5 - - - +
136B THR* 1.3 87.6 - - + +
138B ILE* 1.3 54.6 + - - +
139B PHE* 2.7 4.0 + - + +
140B ASP* 2.5 50.5 + - - +
141B ASN 3.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.3 9.4 - - + +
92B ILE* 4.1 27.4 - - + -
94B VAL* 4.0 26.2 - - + -
99B VAL* 3.8 23.1 - - + -
101B GLN* 2.7 29.3 + - + +
123B VAL* 3.7 29.4 - - + -
124B GLY 4.4 7.5 + - - +
125B MET* 4.7 3.8 - - - -
137B PRO* 1.3 68.7 - - - +
139B PHE* 1.3 69.5 + - + +
140B ASP 3.2 0.7 + - - -
141B ASN* 3.2 3.0 + - - +
142B ILE* 3.2 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY 5.3 0.2 + - - -
125B MET* 4.0 35.0 - - + +
137B PRO* 2.7 7.3 + - + +
138B ILE* 1.3 83.5 - - + +
140B ASP* 1.3 60.2 + - - +
142B ILE* 4.0 9.5 - - + +
143B ILE* 2.9 58.0 + - + +
148B LEU* 3.9 18.4 - - + -
151B ASP* 3.9 7.9 - - - -
152B VAL 3.6 32.8 - - - -
153B PHE* 4.1 13.2 - + + -
171B LEU* 4.0 19.7 - - + -
322B ARG* 3.7 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY 4.9 0.2 - - - +
128B ILE* 4.6 10.6 + - - +
136B THR* 3.5 15.0 - - + +
137B PRO* 2.5 44.4 + - - +
139B PHE* 1.3 73.9 - - - +
141B ASN* 1.3 58.8 + - - +
142B ILE 3.2 0.4 - - - -
143B ILE* 3.4 7.0 + - - +
144B SER* 2.9 31.9 + - - -
322B ARG* 2.6 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.5 25.0 - - + +
100B THR* 3.2 21.2 + - - -
101B GLN* 3.9 16.1 - - - +
136B THR* 3.0 30.7 - - - +
137B PRO 3.6 1.0 + - - -
138B ILE 3.2 7.6 + - - +
140B ASP* 1.3 76.2 - - - +
142B ILE* 1.3 62.3 + - - +
143B ILE 3.4 0.2 - - - -
144B SER* 3.8 13.9 + - - -
145B GLN* 3.8 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 5.1 6.3 - - + -
97B ILE* 3.8 38.4 - - + -
99B VAL* 3.9 17.5 - - + -
138B ILE* 3.2 33.6 + - + +
139B PHE* 4.1 10.5 - - + +
140B ASP 3.2 0.4 - - - -
141B ASN* 1.3 75.7 - - - +
143B ILE* 1.3 64.5 + - - +
145B GLN* 2.8 28.8 + - + +
147B VAL* 4.0 9.7 + - + +
148B LEU* 3.8 23.7 - - + +
171B LEU* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 2.9 35.6 + - + +
140B ASP* 3.5 11.2 - - - +
142B ILE* 1.3 79.0 - - - +
144B SER* 1.3 58.5 + - - +
146B GLY* 2.8 24.3 + - - -
147B VAL 5.6 0.7 - - - +
148B LEU* 3.3 35.4 - - + -
151B ASP* 3.2 34.1 - - - +
322B ARG* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP 2.9 17.0 + - - -
141B ASN* 3.9 12.1 + - - -
142B ILE 3.3 0.4 - - - -
143B ILE* 1.3 80.8 - - - +
145B GLN* 1.3 56.9 + - - +
146B GLY 3.1 1.9 + - - -
----------------------------------------------------------
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