Contacts of the helix formed by residues 157 - 167 (chain F) in PDB entry 4IGM
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 LEU 157 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F MET* 3.7 38.8 - - + +
122F PRO* 4.6 3.8 - - + -
147F VAL* 4.2 11.7 - - + -
150F TRP* 4.4 15.5 - - + -
151F ASP 3.9 22.2 - - - +
152F LEU* 4.1 25.4 - - + -
154F ALA* 3.1 17.4 + - + +
155F GLN 2.9 1.6 + - - -
156F GLU* 1.3 82.4 - - + +
158F PHE* 1.3 64.2 + - - +
159F PRO* 3.3 3.6 - - - -
160F VAL* 3.3 14.2 + - + +
161F TYR* 3.1 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ASN 3.1 24.9 - - - -
154F ALA 3.0 19.1 - - - -
155F GLN* 3.0 48.1 + - - +
157F LEU* 1.3 79.0 - - - +
159F PRO* 1.4 59.8 - - + +
161F TYR* 3.3 8.7 + + - -
162F ALA* 2.8 30.7 + - - +
209F GLY 4.0 17.0 - - - -
210F GLY* 4.9 0.9 - - - -
211F VAL* 4.4 17.3 - - + -
214F LYS* 4.2 23.8 - - + -
215F PHE* 3.6 31.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F PRO* 4.8 9.4 - - + -
123F GLU* 5.6 5.8 - - + -
126F VAL* 4.3 15.4 - - + +
155F GLN 3.5 11.0 - - - +
156F GLU* 3.6 11.0 - - - +
157F LEU 3.3 4.7 - - - -
158F PHE* 1.4 91.4 - - + +
160F VAL* 1.3 56.0 + - - +
162F ALA* 3.1 8.8 + - + +
163F ALA* 2.9 28.9 + - - +
166F ARG* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F LEU* 4.4 2.0 - - + -
119F MET* 4.2 25.8 - - + +
122F PRO* 3.9 35.7 - - + +
125F ALA* 4.4 9.6 - - + -
126F VAL* 4.1 7.5 - - - +
129F MET* 3.5 25.7 - - + +
157F LEU* 3.3 23.1 - - + +
159F PRO* 1.3 73.8 - - - +
161F TYR* 1.3 60.8 + - + +
163F ALA* 3.1 5.0 + - - +
164F ALA* 2.8 28.3 + - + +
171F LEU* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F MET* 5.5 4.9 - - + -
143F ILE* 5.0 5.8 - - + -
152F LEU* 2.6 56.4 + - + +
157F LEU* 3.1 37.0 + - + +
158F PHE* 3.3 12.3 + + - +
160F VAL* 1.3 81.1 - - + +
162F ALA* 1.3 63.6 + - - +
164F ALA* 3.3 6.4 + - - +
165F GLU* 2.9 25.1 + - - +
171F LEU* 4.0 21.8 - - + -
206F MET* 4.2 15.4 - - + +
211F VAL* 3.9 16.8 - - + -
215F PHE* 3.6 25.0 - + + -
218F LEU* 3.9 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F PHE 2.8 14.8 + - - +
159F PRO* 3.1 11.8 + - + +
161F TYR* 1.3 75.8 - - - +
163F ALA* 1.3 53.1 + - - +
165F GLU* 3.3 4.7 + - - +
166F ARG* 2.7 47.7 + - - +
215F PHE* 3.6 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F VAL* 3.7 24.5 - - + -
129F MET* 4.1 12.1 - - - -
159F PRO 2.9 12.4 + - - +
160F VAL* 3.4 9.2 - - - +
162F ALA* 1.3 73.5 - - - +
164F ALA* 1.3 66.6 + - - +
166F ARG* 3.3 23.3 - - - +
167F LEU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F MET* 3.6 18.0 - - + -
160F VAL 2.8 17.1 + - - +
161F TYR* 3.5 11.2 - - - +
163F ALA* 1.3 74.2 - - - +
165F GLU* 1.3 63.7 + - - +
168F LYS* 3.1 2.4 + - - -
169F CYS* 2.9 43.5 + - - +
171F LEU* 4.1 13.9 - - + -
218F LEU* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F TYR 2.9 16.1 + - - +
162F ALA* 3.6 4.4 - - - +
164F ALA* 1.3 76.4 - - - +
166F ARG* 1.3 67.6 + - - +
168F LYS* 3.6 9.3 + - - +
214F LYS 4.6 0.3 - - - +
215F PHE* 3.1 37.9 - - + -
216F PRO* 3.5 5.4 - - - +
217F LYS* 2.8 48.1 + - + +
218F LEU* 3.8 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F VAL* 5.0 5.1 - - - +
130F GLU* 5.9 1.2 + - - -
159F PRO 4.4 2.0 + - - -
162F ALA* 2.7 25.1 + - - +
163F ALA* 3.1 37.4 + - - +
165F GLU* 1.3 77.1 - - - +
167F LEU* 1.3 77.5 + - + +
168F LYS* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F MET* 4.4 10.1 - - + +
130F GLU* 3.8 44.2 - - + +
133F VAL* 4.0 30.4 - - + +
134F LYS* 4.8 19.5 - - + +
163F ALA* 2.9 29.5 + - + +
164F ALA 4.6 0.7 - - - +
166F ARG* 1.3 94.6 - - + +
168F LYS* 1.3 73.1 + - - +
169F CYS* 3.3 4.1 + - + +
----------------------------------------------------------
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