Contacts of the helix formed by residues 123 - 135 (chain B) in PDB entry 4F2N
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 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PRO 3.4 9.4 - - - +
122B MET* 1.3 91.0 - - + +
124B LYS* 1.3 66.3 + - - +
125B THR* 4.4 3.4 - - - +
126B LEU* 3.1 5.7 + - - +
127B GLU* 3.1 17.7 + - - +
218B TRP 3.6 18.4 - - - +
219B GLU* 4.3 14.4 - - + -
222B CYS* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET 3.7 1.0 + - - -
123B PRO* 1.3 72.3 - - - +
125B THR* 1.3 64.1 + - - +
127B GLU* 2.9 33.2 + - - +
128B ASN* 3.0 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 3.2 3.2 + - - +
124B LYS* 1.3 78.2 - - - +
126B LEU* 1.3 63.3 + - - +
128B ASN* 3.6 8.5 + - - +
129B ALA* 3.2 22.0 + - - +
222B CYS* 4.1 6.5 - - - -
225B TYR* 4.3 21.8 - - + -
226B GLU* 3.8 26.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
122B MET* 3.8 9.6 - - + -
123B PRO 3.1 9.2 + - - +
125B THR* 1.3 78.2 - - - +
127B GLU* 1.3 65.5 + - - +
129B ALA* 3.1 4.5 + - + +
130B ILE* 2.9 43.1 + - + +
168B LEU* 5.4 0.4 - - + -
187B ILE* 4.4 11.4 - - + -
218B TRP* 3.6 26.9 - - + +
221B VAL* 3.6 24.0 - - + -
222B CYS* 3.8 26.0 - - + +
225B TYR* 4.1 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 3.6 23.3 - - + +
123B PRO 3.1 12.5 + - - +
124B LYS* 2.9 41.7 + - + +
126B LEU* 1.3 75.9 - - - +
128B ASN* 1.3 58.9 + - - +
130B ILE* 3.4 1.6 + - - +
131B ALA* 2.9 32.7 + - + +
137B VAL* 3.9 20.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
124B LYS* 3.0 48.1 + - - +
125B THR* 3.7 6.8 - - - +
127B GLU* 1.3 77.5 - - - +
129B ALA* 1.3 57.6 + - - +
131B ALA* 3.4 5.4 + - - +
132B LYS* 2.8 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR 3.2 9.9 + - - +
126B LEU* 3.1 10.1 + - + +
128B ASN* 1.3 79.5 - - - +
130B ILE* 1.3 62.3 + - - +
132B LYS* 3.4 10.3 + - - +
133B GLN* 3.2 18.5 + - - +
168B LEU* 3.6 14.3 - - + +
225B TYR* 3.4 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 4.1 20.2 - - + -
126B LEU* 2.9 46.3 + - + +
127B GLU 3.9 2.9 - - - +
129B ALA* 1.3 73.4 - - - +
131B ALA* 1.3 60.6 + - - +
133B GLN 3.3 0.9 + - - -
134B PHE* 2.9 33.8 + - + +
136B SER 4.3 0.2 - - - +
137B VAL* 4.0 17.5 - - + -
140B PHE* 3.5 39.0 - - + -
159B LEU* 4.3 19.3 - - + -
168B LEU* 4.1 13.5 - - + -
218B TRP* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU* 2.9 21.1 + - + +
128B ASN* 3.9 5.2 - - - +
130B ILE* 1.3 76.2 - - - +
132B LYS* 1.3 60.5 + - - +
135B GLY* 2.8 40.6 + - - +
136B SER* 3.9 19.0 - - - +
137B VAL* 4.7 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASN 2.8 19.6 + - - +
129B ALA* 3.7 9.6 - - - +
130B ILE 3.3 0.2 - - - -
131B ALA* 1.3 78.8 - - - +
133B GLN* 1.3 59.6 + - - +
135B GLY 4.7 0.5 + - - -
225B TYR* 5.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.2 14.2 + - - +
132B LYS* 1.3 78.6 - - - +
134B PHE* 1.3 87.4 + - + +
135B GLY 3.5 0.4 + - - -
167B GLU* 3.5 24.4 + - - +
168B LEU* 3.0 45.9 + - + +
169B LEU* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 2.9 30.5 + - + +
133B GLN* 1.3 93.0 - - + +
135B GLY* 1.3 57.2 + - - +
136B SER 3.3 6.8 + - - +
139B ASP* 3.4 17.4 - - - +
140B PHE* 3.7 48.0 - + + +
143B SER* 5.2 5.4 - - - -
159B LEU* 4.0 17.7 - - + -
168B LEU* 3.8 32.8 - - + -
169B LEU* 4.4 0.7 - - - -
170B ILE* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 2.8 23.5 + - - +
132B LYS 4.7 0.4 + - - -
133B GLN 3.5 1.8 + - - -
134B PHE* 1.3 75.2 - - - +
136B SER* 1.3 61.2 + - - +
139B ASP* 4.2 4.9 - - - -
----------------------------------------------------------
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