Contacts of the helix formed by residues 87 - 97 (chain A) in PDB entry 3E6G
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 SER 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.1 2.9 + - - +
86A ALA* 1.3 79.7 - - - +
88A GLY* 1.3 65.1 + - - +
89A MET* 3.5 6.1 + - - +
90A ALA* 3.2 13.1 + - - +
91A ALA 3.1 16.6 + - - -
219A VAL* 3.4 17.5 - - - -
220A GLY* 3.4 8.7 - - - -
221A GLY* 3.1 13.2 + - - -
243B GLY* 2.5 31.0 + - - -
245B VAL* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 1.3 72.1 - - - +
89A MET* 1.3 63.3 + - - +
91A ALA* 3.0 5.9 + - - +
92A THR* 3.0 29.1 + - - -
205A VAL* 5.9 0.5 - - - +
206A HIS 4.2 2.5 - - - -
207A SER* 4.0 24.5 - - - +
209A THR* 4.7 2.8 + - - -
220A GLY 3.4 4.6 + - - +
221A GLY* 3.4 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.2 11.1 + - - +
88A GLY* 1.3 78.0 - - - +
90A ALA* 1.3 52.9 + - - +
92A THR* 3.1 21.5 + - - +
93A SER* 2.6 34.8 + - - -
112A TYR* 3.6 24.2 - - + +
114A GLY* 3.8 23.8 - - - +
115A THR* 3.2 29.4 - - - +
117A ARG* 5.9 1.3 - - - +
118A LEU* 4.9 3.3 - - - +
240B ASN 4.8 6.3 - - - +
241B SER* 3.9 24.0 - - - +
242B ILE 3.3 6.3 - - - +
243B GLY* 4.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.0 3.9 - - + -
87A SER* 3.2 16.5 + - - +
89A MET* 1.3 72.2 - - - +
91A ALA* 1.3 66.0 + - - +
93A SER* 3.4 2.0 - - - -
94A THR* 3.0 30.1 + - - +
244A GLY* 4.0 25.4 - - - +
242B ILE* 3.1 13.8 + - + +
243B GLY 3.7 20.0 - - - +
244B GLY* 4.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.3 30.6 - - + +
87A SER 3.1 10.5 + - - +
88A GLY 3.0 11.2 + - - +
90A ALA* 1.3 77.4 - - - +
92A THR* 1.3 58.2 + - - +
94A THR* 3.3 1.0 + - - -
95A VAL* 2.6 37.6 + - + +
205A VAL* 4.9 7.0 - - + -
206A HIS 4.5 2.5 - - - +
221A GLY* 4.1 1.1 - - - -
222A ILE 4.0 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY 3.0 12.6 + - - -
89A MET* 3.6 23.2 - - + +
91A ALA* 1.3 78.1 - - - +
93A SER* 1.3 65.5 + - - +
95A VAL* 3.0 8.4 + - - +
96A MET* 3.0 23.6 + - - +
115A THR* 4.2 17.6 + - + +
118A LEU* 3.6 22.0 - - + -
119A PHE* 4.3 4.5 - - + -
154A TRP* 3.4 32.3 - - + -
185A ASP* 5.2 0.9 + - - -
205A VAL* 4.3 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET 2.6 26.1 + - - -
90A ALA* 3.4 4.6 - - - -
92A THR* 1.3 72.5 - - - +
94A THR* 1.3 63.4 + - - +
96A MET* 3.2 9.6 + - - +
97A GLU* 3.3 3.3 - - - +
118A LEU* 4.0 22.8 - - - +
123A ARG* 2.9 33.2 + - - +
242B ILE* 2.6 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.8 18.1 - - + -
90A ALA* 3.0 19.7 + - - +
93A SER* 1.3 75.6 - - - +
95A VAL* 1.3 64.6 + - - +
97A GLU* 3.0 22.1 + - + +
98A LEU 3.8 2.1 + - - -
235A MET* 4.6 4.3 - - + -
238A LEU* 3.9 15.4 - - + +
239A GLN* 3.7 21.3 - - - +
242A ILE* 3.0 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 2.6 38.4 + - - +
92A THR* 3.5 6.3 - - - +
94A THR* 1.3 76.9 - - - +
96A MET* 1.3 56.4 + - - +
98A LEU* 2.8 40.1 - - + +
152A MET* 5.0 5.1 - - - +
154A TRP* 4.2 19.1 - - + -
183A VAL* 4.5 15.0 - - + -
203A LEU* 4.7 7.4 - - + -
205A VAL* 3.9 22.9 - - + -
223A ALA* 4.5 4.0 - - + -
235A MET* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR 3.0 9.9 + - - +
93A SER* 3.4 13.7 - - - +
95A VAL* 1.3 74.7 - - - +
97A GLU* 1.3 56.6 + - - +
98A LEU 2.9 5.4 - - - -
99A LEU* 3.1 32.2 + - + +
105A VAL* 3.5 24.7 - - + -
118A LEU* 4.6 3.8 - - + -
119A PHE* 3.4 37.5 - - + -
123A ARG* 4.3 13.7 - - + +
129A LEU* 4.7 13.5 - - + +
131A PHE* 3.8 7.0 - - + -
152A MET* 3.3 38.6 - - + +
154A TRP* 3.9 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 3.3 7.8 - - - +
94A THR* 3.0 10.3 + - - +
96A MET* 1.3 73.9 - - - +
98A LEU* 1.3 65.5 + - - +
99A LEU* 2.9 2.7 - - - +
123A ARG* 2.9 33.8 + - - +
238A LEU* 3.8 16.2 - - + +
242A ILE* 4.1 15.4 - - + +
93B SER* 5.8 0.2 - - - -
97B GLU* 4.3 0.7 - - - +
122B VAL* 3.8 8.1 - - - +
123B ARG* 2.6 36.4 + - - -
125B ARG* 3.1 20.8 + - - -
126B THR* 2.9 31.6 + - + +
----------------------------------------------------------
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