Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 5I75
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 PHE 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.3 6.7 - + - -
108A ILE* 4.2 28.0 - - + -
109A CYS* 3.7 26.2 - - + +
112A ASN* 3.2 42.6 + - + +
114A GLY 2.9 15.2 + - - +
116A ALA* 1.3 77.9 - - - +
118A LEU* 1.3 61.5 + - - +
119A LEU 3.1 0.4 - - - -
120A PRO* 3.2 10.5 - - + +
121A TYR* 3.2 38.6 + + + +
320A LEU* 5.5 0.4 - - - -
325A VAL* 3.9 13.7 - - + -
329A ALA* 3.6 39.0 - - + -
332A GLN* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.1 19.5 - - + -
109A CYS* 4.7 7.4 - - - -
115A GLY* 2.9 26.2 + - - +
117A PHE* 1.3 80.8 - - - +
119A LEU* 1.3 62.7 + - - +
121A TYR* 3.9 8.2 - - + +
122A THR* 3.3 29.3 + - + +
313A LEU* 5.2 4.9 - - + -
373A PHE* 3.5 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 4.4 0.2 + - - -
116A ALA* 3.1 11.0 + - - +
118A LEU* 1.3 78.8 - - - +
120A PRO* 1.3 68.1 - - + +
122A THR* 2.9 20.8 + - - -
123A ILE* 3.3 31.4 - - + +
317A TRP* 4.4 20.6 - - + -
320A LEU* 4.1 17.3 - - + -
326A TRP* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA 3.1 14.6 - - - +
117A PHE* 3.2 22.9 - - + +
119A LEU* 1.3 91.6 - - + +
121A TYR* 1.3 63.0 + - - +
122A THR 3.3 0.2 - - - -
123A ILE* 4.0 1.1 - - + +
124A MET* 3.1 29.6 + - - +
320A LEU* 3.7 19.5 - - + -
325A VAL* 5.1 4.7 - - + +
326A TRP* 3.6 42.8 - - + -
329A ALA* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.9 37.6 - + - -
117A PHE* 3.2 38.0 + + + +
118A LEU* 3.9 9.6 - - + +
119A LEU 3.2 0.2 - - - -
120A PRO* 1.3 79.6 - - - +
122A THR* 1.3 71.2 + - + +
124A MET* 3.9 3.8 + - - +
125A ALA* 3.5 17.9 + - + +
329A ALA* 4.1 13.5 - - - -
332A GLN* 4.0 19.6 + - + +
333A ILE* 3.3 34.0 - - + +
336A SER* 4.8 4.3 + - - -
368A ASN* 4.7 3.3 + - - -
369A CYS* 3.8 34.8 - - + +
372A SER* 4.3 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.3 18.1 + - + +
119A LEU* 2.9 17.5 + - - -
121A TYR* 1.3 86.0 - - + +
123A ILE* 1.3 62.5 + - - +
124A MET 3.2 0.2 - - - -
125A ALA* 2.9 7.3 + - - +
126A ILE* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.3 29.8 + - + +
120A PRO 3.5 4.0 + - - +
122A THR* 1.3 78.8 + - - +
124A MET* 1.3 64.6 + - + +
126A ILE* 4.2 4.9 - - + -
127A PHE* 3.2 52.5 + - + +
326A TRP* 3.9 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO 3.1 18.2 + - - +
121A TYR 4.2 2.5 - - - +
122A THR 3.2 0.2 - - - -
123A ILE* 1.3 80.1 - - + +
125A ALA* 1.3 57.4 + - - +
127A PHE* 6.3 1.1 - - - -
128A GLY* 3.2 9.7 + - - +
129A GLY 2.9 19.1 + - - -
326A TRP* 3.5 47.1 - - + +
329A ALA* 4.2 2.2 - - + -
330A ALA* 3.6 33.9 - - + +
333A ILE* 3.6 8.4 - - + +
548A PHE* 3.4 28.1 - - + -
551A PHE* 5.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.5 9.4 + - + +
122A THR* 2.9 11.7 + - - +
124A MET* 1.3 77.4 - - - +
126A ILE* 1.3 66.5 + - + +
127A PHE 3.2 1.1 - - - -
129A GLY* 2.9 9.1 + - - +
130A ILE* 2.6 42.0 + - + -
333A ILE* 3.7 26.7 - - + -
337A LEU* 5.0 0.2 - - + -
369A CYS* 5.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 2.9 32.3 + - - +
123A ILE* 4.4 4.0 - - - +
125A ALA* 1.3 73.7 - - + +
127A PHE* 1.3 73.0 + - + +
130A ILE* 3.9 11.6 - - + +
131A PRO* 3.3 19.1 - - - +
536A PHE* 3.5 33.3 - - + -
537A TRP* 4.8 1.1 - - + -
540A CYS* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.2 39.4 + - + +
124A MET* 5.3 1.3 - - - -
126A ILE* 1.3 94.3 - - + +
128A GLY* 1.3 58.3 + - - +
131A PRO* 3.4 12.8 - - - +
536A PHE* 3.9 25.1 - + - -
540A CYS* 4.0 7.3 - - - -
544A ILE* 3.1 38.6 - - + +
545A SER* 3.9 3.8 + - - -
548A PHE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET 3.2 12.2 + - - -
127A PHE* 1.3 80.2 - - - +
129A GLY* 1.3 65.8 + - - +
131A PRO* 3.5 2.0 - - - +
132A LEU* 3.4 28.9 + - - +
545A SER* 4.1 2.1 + - - -
548A PHE* 3.6 33.1 - - - -
----------------------------------------------------------
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