Contacts of the helix formed by residues 124 - 134 (chain A) in PDB entry 2O2C
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 GLY 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA 3.4 0.2 + - - -
121A GLU 3.2 14.3 + - - -
122A GLU 3.2 2.0 + - - -
123A ARG* 1.3 79.3 - - - +
125A ILE* 1.3 59.2 + - - +
126A ARG 3.4 2.0 - - - -
127A GLN* 3.4 24.1 + - - +
128A PHE* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.1 36.1 + - + +
123A ARG* 4.5 8.3 - - + +
124A GLY* 1.3 74.5 - - - +
126A ARG* 1.3 59.9 - - - +
128A PHE* 3.2 4.2 + - + +
129A VAL* 2.9 46.0 + - + +
360A PHE* 5.2 0.9 - - + -
371A LEU* 3.9 20.6 - - + -
551A LEU* 5.4 1.1 - - + -
552A VAL* 4.0 24.0 - - + +
555A ALA* 3.6 32.5 - - + -
556A ILE* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA 4.9 0.8 + - - -
121A GLU* 4.8 24.4 + - - +
124A GLY 3.4 0.8 - - - -
125A ILE* 1.3 77.3 - - - +
127A GLN* 1.3 87.7 + - + +
129A VAL* 3.5 6.9 + - - +
130A GLN* 3.2 35.2 + - + +
361A ALA 6.0 1.6 - - - +
365A PRO* 5.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU 5.0 3.2 + - - +
124A GLY* 3.4 27.1 - - - +
125A ILE 3.3 0.2 - - - -
126A ARG* 1.3 101.2 + - + +
128A PHE* 1.3 59.8 + - - +
130A GLN* 3.4 8.3 + - - +
131A SER* 3.0 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG 5.6 0.9 - - - +
124A GLY 3.0 17.9 + - - +
125A ILE* 3.6 8.1 - - + +
127A GLN* 1.3 73.4 - - - +
129A VAL* 1.3 59.0 + - - +
131A SER* 3.2 8.6 + - - -
132A VAL* 3.0 50.2 + - + +
138A VAL* 4.1 27.6 - - + -
419A ARG* 3.3 36.1 - - - -
551A LEU* 3.7 28.7 - - + -
555A ALA* 3.7 24.2 - - + -
559A ILE 5.8 0.7 - - - -
562A TYR* 4.7 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 2.9 28.3 + - + +
126A ARG* 3.6 7.4 - - - +
128A PHE* 1.3 73.9 - - - +
130A GLN* 1.3 63.5 + - - +
132A VAL* 3.2 7.1 + - - +
133A PHE* 3.0 42.9 + - + -
360A PHE* 3.5 47.6 - - + +
361A ALA* 4.2 20.0 - - + -
551A LEU* 3.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.2 22.0 + - + +
127A GLN* 3.7 10.8 - - - +
129A VAL* 1.3 79.8 - - - +
131A SER* 1.3 57.0 + - - +
133A PHE* 3.4 6.8 + - - +
134A ARG* 3.0 81.1 + - - +
361A ALA* 3.7 35.4 + - - +
362A ASN* 5.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN* 3.0 15.3 + - - +
128A PHE* 3.4 14.2 - - - -
129A VAL 3.2 0.2 - - - -
130A GLN* 1.3 77.3 - - - +
132A VAL* 1.3 60.3 + - - +
134A ARG* 3.6 1.3 + - - +
135A GLY 3.4 3.3 + - - -
136A GLU* 2.9 53.8 + - - +
138A VAL* 4.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.0 44.1 + - + +
129A VAL 3.2 6.5 + - - +
131A SER* 1.3 75.4 - - - +
133A PHE* 1.3 69.3 + - + +
135A GLY* 3.3 12.0 + - - -
136A GLU 4.6 1.8 + - - +
138A VAL* 4.0 22.9 - - + -
146A VAL* 3.4 31.4 - - + +
147A LEU* 3.4 13.3 - - - +
148A HIS* 5.4 4.7 - - + +
149A ILE* 5.5 4.5 - - + -
551A LEU* 4.1 23.3 - - + -
562A TYR* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.0 36.1 + - + +
130A GLN* 3.9 9.0 - - - +
132A VAL* 1.3 88.4 - - + +
134A ARG* 1.3 60.4 + - + +
135A GLY 3.6 0.3 + - - -
147A LEU* 3.8 4.7 - - - +
149A ILE* 3.7 54.7 - - + +
157A ARG* 4.3 16.2 + - - +
159A ILE* 3.8 11.8 - - - +
357A ASP* 3.5 42.2 - - + -
358A GLU* 5.1 3.6 - - - -
360A PHE* 4.2 9.0 - + - -
361A ALA* 3.9 13.5 - - + -
548A HIS* 4.0 15.7 - + - -
551A LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN* 3.0 57.8 + - - +
131A SER* 4.3 4.5 - - - +
132A VAL 3.3 0.4 - - - -
133A PHE* 1.3 78.7 - - + +
135A GLY* 1.3 59.5 + - - +
136A GLU* 3.6 6.7 + - + +
159A ILE* 4.4 8.4 - - - +
160A TYR* 4.0 13.7 + - - +
188B GLU* 3.4 47.2 + - + +
7004B GOL 4.6 12.3 + - - -
----------------------------------------------------------
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