Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 2G1Y
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 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.5 23.5 + - - -
126A GLY* 1.3 72.8 - - - -
128A ILE* 1.3 66.0 + - - +
129A GLU* 3.4 8.5 - - - +
130A GLN* 3.0 8.6 + - - +
137A PRO* 4.1 1.1 - - - -
140A ASP* 5.5 0.2 - - - -
190A LEU* 3.8 16.6 - - + -
193A THR* 3.4 18.2 - - - -
194A GLY* 3.3 42.6 + - - +
195A VAL* 3.4 15.3 - - - -
196A TRP* 3.3 41.5 - + - -
324A ARG* 3.2 48.2 - - - +
327A ASN* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 1.3 73.3 - - - +
129A GLU* 1.3 73.7 + - - +
131A ALA* 2.8 25.0 + - + +
134A ARG* 4.5 16.6 - - + +
135A VAL 4.1 6.3 - - - +
136A THR* 4.3 14.8 - - + +
137A PRO* 3.4 36.5 - - + +
140A ASP* 3.8 12.2 + - - +
324A ARG* 5.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.0 7.2 - - - +
128A ILE* 1.3 98.3 + - + +
130A GLN* 1.3 69.9 + - - +
131A ALA 3.4 1.8 + - - +
192A LYS* 4.6 4.8 + - - +
193A THR* 3.8 18.7 + - - +
194A GLY* 3.5 36.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
36A SER* 5.7 2.9 - - - -
37A SER* 3.7 21.7 + - - +
38A ASN* 4.6 0.5 - - - +
126A GLY* 5.9 0.2 - - - -
127A PHE 3.0 3.5 + - - +
128A ILE 3.0 0.8 - - - -
129A GLU* 1.3 89.1 + - - +
131A ALA* 1.3 63.1 + - - +
132A ILE* 3.4 13.8 + - - +
194A GLY 3.1 19.9 + - - +
195A VAL* 3.8 23.3 - - + +
303A PRO* 4.9 14.2 - - - +
304A THR* 4.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.7 19.3 - - - +
38A ASN* 3.7 4.5 - - - +
127A PHE 3.6 1.2 + - - -
128A ILE* 2.8 24.5 + - + +
129A GLU 3.4 1.6 - - - +
130A GLN* 1.3 75.7 - - - +
132A ILE* 1.3 65.9 + - - +
133A GLY 3.3 0.7 + - - -
134A ARG* 3.1 13.8 + - - +
135A VAL* 3.4 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.0 31.3 + - - +
74A LEU* 4.4 15.8 - - + +
75A THR 3.6 22.2 - - - +
76A LEU* 4.0 22.2 - - + -
77A ARG 5.6 1.6 - - - +
130A GLN 4.2 10.1 - - - +
131A ALA* 1.3 71.8 - - - +
133A GLY* 1.3 65.3 + - - +
134A ARG 3.5 0.2 + - - -
135A VAL* 3.7 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 6.3 2.5 - - - -
74A LEU* 5.9 3.4 - - - -
87A LEU* 5.4 5.2 - - - +
131A ALA 3.3 1.0 + - - -
132A ILE* 1.3 75.1 - - - +
134A ARG* 1.3 86.9 + - - +
135A VAL* 3.1 12.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
128A ILE* 4.5 14.9 - - + +
131A ALA* 3.1 17.6 + - - +
133A GLY* 1.3 87.5 + - - +
135A VAL* 1.3 62.5 + - - +
136A THR* 3.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER 4.8 1.4 - - - +
38A ASN* 4.1 19.1 - - - +
87A LEU* 3.8 32.8 - - + -
101A GLN* 4.7 0.4 - - - +
102A MET* 3.4 46.4 - - + +
128A ILE* 4.1 1.0 - - - +
131A ALA* 3.4 14.1 - - - +
132A ILE 3.7 16.6 + - - +
133A GLY 3.8 6.7 - - - +
134A ARG* 1.3 76.5 - - - +
136A THR* 1.3 71.6 + - - +
137A PRO* 3.1 10.3 - - - +
----------------------------------------------------------
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