Contacts of the helix formed by residues 124 - 130 (chain L) in PDB entry 3J7Y
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 124 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L VAL* 3.7 31.0 - - + -
87L VAL* 4.1 11.4 - - + -
88L GLY 4.6 0.9 - - - +
97L THR* 6.0 0.4 - - - -
98L PRO* 3.7 31.4 - - + +
100L PHE* 3.8 20.4 - - + -
123L ILE* 1.4 102.5 - - + +
125L THR* 1.3 63.9 + - - +
126L SER* 3.3 12.4 + - - +
127L LEU* 3.6 8.2 + - + -
144L PHE* 3.9 4.7 - - - -
145L VAL* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L PRO* 5.3 1.8 - - - +
123L ILE 3.8 0.2 + - - -
124L PRO* 1.3 72.3 - - - +
126L SER* 1.3 64.8 + - - +
128L ARG* 3.1 28.3 + - - +
144L PHE* 4.3 15.3 - - + -
145L VAL 3.4 35.0 - - - +
123Q ASP* 4.4 16.6 + - + +
125Q TYR* 3.6 25.1 + - - +
126Q ALA* 5.0 3.8 - - + -
131Q SER* 4.8 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L VAL* 4.2 12.6 + - - +
97L THR* 4.9 17.3 - - - +
124L PRO* 3.8 18.7 - - - +
125L THR* 1.3 80.2 + - - +
127L LEU* 1.3 58.4 + - - +
128L ARG 3.1 0.2 - - - -
129L LYS* 3.0 44.4 + - - +
130L ARG* 4.8 0.3 + - - -
125Q TYR* 5.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L VAL* 4.2 11.2 - - + -
70L GLY* 3.9 32.1 - - - +
85L LEU* 4.3 18.2 - - + -
86L ILE 4.6 0.4 - - - +
87L VAL* 3.9 24.7 - - + -
123L ILE* 3.4 29.6 - - + -
124L PRO* 3.6 8.6 + - + +
125L THR 3.1 1.4 + - - -
126L SER* 1.3 81.0 + - - +
128L ARG* 1.3 59.5 + - - +
129L LYS 3.2 0.2 - - - -
130L ARG* 3.3 29.7 - - - +
134L TYR* 4.8 6.2 - - + +
137L VAL* 5.3 4.5 - - + -
138L LEU* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L THR* 3.1 17.5 + - - +
127L LEU* 1.3 75.1 - - - +
129L LYS* 1.3 63.9 + - - +
130L ARG 3.2 1.5 + - - -
131L GLU* 3.5 29.8 + - - +
138L LEU* 3.8 25.5 + - + +
144L PHE* 3.2 56.2 - - + +
125Q TYR* 3.7 33.2 + - + +
126Q ALA* 3.6 22.1 - - - +
127Q SER* 4.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3141A A 5.2 7.9 + - - -
69L VAL 5.6 2.9 - - - -
126L SER* 3.0 28.9 + - - +
128L ARG* 1.3 78.7 - - - +
130L ARG* 1.3 95.9 + - - +
131L GLU* 4.7 0.9 - - - +
125Q TYR* 3.3 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L VAL 4.7 2.4 + - - -
70L GLY* 3.5 35.9 + - - -
71L ASP* 4.4 10.1 + - - +
126L SER 5.3 0.4 + - - -
127L LEU* 3.3 28.0 - - - +
129L LYS* 1.3 117.1 - - - +
131L GLU* 1.3 71.9 + - - +
133L GLU* 3.6 32.2 - - + +
134L TYR* 3.4 32.2 + - + +
----------------------------------------------------------
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