Contacts of the helix formed by residues 121 - 129 (chain B) in PDB entry 3P9K
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 MET 121 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 4.0 21.1 - - - +
20A ALA* 4.2 22.2 - - + +
21A LEU* 3.4 37.7 - - + -
24A ALA* 3.6 10.1 - - + +
111B PHE* 2.9 21.6 + - + +
112B LEU* 4.3 5.0 - - + +
120B SER* 1.3 77.3 - - - +
122B ALA* 1.3 62.0 + - - +
123B ALA 3.4 0.9 - - - -
124B LEU* 3.4 15.8 + - + +
125B ALA* 3.4 14.4 + - - +
180B HIS* 4.2 17.7 - - + -
183B ILE* 3.3 42.0 - - + -
184B ILE* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.1 23.5 - - + +
111B PHE 4.2 1.6 + - - -
112B LEU* 3.5 20.4 - - - +
120B SER* 3.0 17.0 + - - +
121B MET* 1.3 76.9 - - - +
123B ALA* 1.3 66.7 + - - +
125B ALA* 2.9 19.4 + - - +
126B LEU* 3.0 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER 4.1 1.6 + - - -
121B MET 3.4 0.4 - - - -
122B ALA* 1.3 78.8 - - - +
124B LEU* 1.3 57.1 + - - +
126B LEU* 3.2 12.8 + - - +
127B MET* 2.9 27.5 + - - +
172B VAL* 4.7 2.3 - - - +
175B GLU* 3.7 10.5 - - + +
176B GLY* 3.6 25.2 - - - +
179B ASN* 3.7 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.6 30.3 - - + -
24A ALA* 3.9 8.3 - - + -
120B SER 5.1 0.9 + - - +
121B MET* 3.4 15.8 + - - +
122B ALA 3.2 0.6 - - - -
123B ALA* 1.3 79.0 - - - +
125B ALA* 1.3 58.0 + - - +
127B MET* 3.5 15.0 - - + +
128B ASN* 2.9 41.1 + - - +
176B GLY 3.7 17.0 - - - +
177B MET* 3.6 32.1 - - + -
179B ASN* 6.0 0.2 - - + -
180B HIS* 3.9 21.8 - - + +
263B TRP* 4.5 2.2 - - + -
602B CIY 4.2 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 5.1 1.1 - - - +
24A ALA* 3.4 28.7 - - + +
33B LEU* 5.3 5.4 - - + -
34B LYS* 4.5 5.3 - - - +
37B ILE* 3.8 23.3 - - + -
112B LEU* 5.6 2.0 - - + -
121B MET 3.4 4.7 + - - +
122B ALA* 2.9 11.1 + - - +
124B LEU* 1.3 80.4 - - - +
126B LEU* 1.3 62.3 + - - +
129B GLN* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 4.0 24.5 + - + +
37B ILE* 4.0 19.7 - - + -
38B GLU* 3.6 35.2 - - + +
122B ALA* 3.0 15.9 + - + +
123B ALA* 3.6 12.8 - - - +
125B ALA* 1.3 78.7 - - - +
127B MET* 1.3 61.6 + - - +
129B GLN 4.0 1.0 - - - -
130B ASP* 3.4 24.9 + - - +
172B VAL* 4.1 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA 2.9 16.5 + - - +
124B LEU* 3.5 25.4 - - + +
125B ALA 3.2 0.2 - - - -
126B LEU* 1.3 74.7 - - - +
128B ASN* 1.3 92.7 + - - +
130B ASP* 3.1 19.1 + - - +
133B LEU* 3.6 19.6 - - + +
169B PHE* 4.2 2.8 - - + -
172B VAL* 3.5 24.8 - - + +
173B PHE* 3.7 32.3 - - + +
176B GLY* 4.7 1.3 - - - -
177B MET* 3.6 19.7 - - + -
602B CIY 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.1 23.9 + - - +
25A SER* 3.8 6.3 - - - -
27A SER* 4.2 3.9 + - - +
124B LEU* 2.9 25.8 + - - +
127B MET* 1.3 92.4 - - - +
129B GLN* 1.3 66.1 + - - +
130B ASP 3.2 2.1 + - - -
133B LEU* 4.0 19.0 - - - +
134B MET* 3.8 14.2 - - - +
137B TRP* 5.3 2.3 + - - -
316B ILE* 3.7 26.0 - - + +
320B HIS* 5.5 0.2 + - - -
602B CIY 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 4.6 2.2 + - - -
24A ALA 2.9 26.2 + - - +
25A SER* 4.1 0.2 - - - -
26A SER 4.0 1.0 + - - -
27A SER* 2.8 36.2 + - - -
138A TYR* 3.7 10.0 - - - -
30B PRO* 4.0 24.4 + - + +
31B MET* 3.9 21.2 - - - +
34B LYS* 2.9 34.3 - - + +
125B ALA* 2.8 35.6 + - - +
127B MET 3.3 0.8 - - - -
128B ASN* 1.3 80.6 - - - +
130B ASP* 1.3 64.7 + - - +
131B LYS 3.7 0.5 + - - -
134B MET* 4.0 8.1 - - - +
----------------------------------------------------------
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