Contacts of the helix formed by residues 134 - 147 (chain A) in PDB entry 5G49
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 TYR 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 3.6 24.9 - - - -
126A MET* 3.8 18.6 - - + -
131A PHE* 3.0 41.5 + + + +
133A ASP* 1.3 85.0 - - + +
135A ILE* 1.3 64.5 + - + +
136A GLU 3.5 0.4 - - - -
137A PRO* 3.3 3.3 - - - +
138A LEU* 3.2 26.5 + - + +
57B PHE* 3.6 16.2 - + - -
100B ALA 4.5 1.1 - - - -
103B MET* 3.9 26.4 - - + +
104B PHE* 3.5 40.9 - - + +
107B GLU* 2.6 30.2 + - - +
138B ILE* 4.3 5.8 - - + -
139B PHE* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.0 18.1 - - + +
126A MET* 3.8 16.6 - - + -
127A SER* 3.7 38.8 - - - +
131A PHE 3.5 18.4 - - - +
132A ASP* 3.4 15.6 + - - +
134A TYR* 1.3 79.3 - - + +
136A GLU* 1.3 60.0 + - - +
138A LEU* 3.2 4.4 + - - +
139A THR* 2.8 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP 4.8 2.0 + - - -
135A ILE* 1.3 80.7 - - - +
137A PRO* 1.3 69.7 - - + +
139A THR* 3.4 5.2 + - - -
140A LEU* 3.0 45.2 + - + +
1151B ACT 4.7 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP 3.7 19.3 - - - +
134A TYR 3.3 10.5 - - - +
136A GLU* 1.3 95.1 - - + +
138A LEU* 1.3 57.2 + - - +
140A LEU* 3.5 3.0 + - + +
141A TYR* 3.0 29.7 + - - +
57B PHE* 4.2 20.9 - - + +
99B ARG* 5.0 5.4 + - - +
103B MET* 4.0 16.6 - - + -
1151B ACT 3.8 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.7 20.1 - - + +
126A MET* 3.5 40.6 - - + -
134A TYR* 3.2 24.6 + - + +
135A ILE* 3.9 0.7 - - - +
137A PRO* 1.3 74.9 - - - +
139A THR* 1.3 56.7 + - - +
141A TYR* 3.3 8.5 + - + +
142A LEU* 2.7 31.8 + - - +
96B VAL* 3.7 16.1 - - + +
99B ARG* 3.8 20.2 - - + -
100B ALA* 3.6 32.3 - - + +
103B MET* 3.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.9 19.2 - - + +
135A ILE* 2.8 32.0 + - - +
136A GLU* 3.8 6.7 - - - -
138A LEU* 1.3 77.0 - - - +
140A LEU* 1.3 57.6 + - + +
142A LEU* 3.3 4.6 + - - -
143A HIS* 2.9 63.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 3.0 49.8 + - + +
137A PRO 4.1 2.2 - - - +
139A THR* 1.3 74.6 - - + +
141A TYR* 1.3 60.8 + - - +
143A HIS* 3.2 9.8 + - + +
144A ARG* 2.9 31.9 + - - +
1151B ACT 4.2 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO 3.0 18.0 + - - +
138A LEU* 3.6 11.2 - - + +
140A LEU* 1.3 78.1 - - - +
142A LEU* 1.3 62.2 + - + +
144A ARG* 3.4 17.8 + - - +
145A TYR* 3.0 29.7 + - + +
68B ASN* 3.9 17.0 - - + -
69B HIS* 4.0 14.7 - - - +
95B VAL* 2.8 45.5 + - + +
96B VAL* 4.2 6.5 - - + -
99B ARG* 3.4 57.3 - - + +
1150B ACT 3.4 27.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 3.8 26.5 - - + -
120A GLU* 4.1 4.7 - - - +
123A LEU* 3.7 26.5 - - + -
138A LEU 2.7 21.2 + - - +
139A THR* 3.6 4.5 - - - +
141A TYR* 1.3 78.2 - - + +
143A HIS* 1.3 68.2 + - + +
145A TYR* 3.4 21.9 + - + +
146A ARG* 3.2 57.7 + - - +
92B GLU* 4.5 5.8 - - + +
95B VAL* 5.5 1.3 - - + -
96B VAL* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 5.4 2.0 + - - -
123A LEU* 6.0 0.2 - - - +
139A THR* 2.9 47.9 + - + +
140A LEU* 3.2 9.3 + - + +
142A LEU* 1.3 90.2 - - + +
144A ARG* 1.3 62.4 + - - +
146A ARG* 3.3 28.1 + - - +
147A GLU* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 2.9 16.1 + - - +
141A TYR* 4.1 12.9 + - - +
143A HIS* 1.3 74.7 - - - +
145A TYR* 1.3 66.0 - - - +
147A GLU* 2.9 39.1 + - - +
59B GLU* 2.7 42.1 + - - -
61B GLU* 3.9 11.5 + - - -
68B ASN* 3.3 36.9 + - - +
99B ARG* 4.3 4.0 - - - +
1150B ACT 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.0 20.2 + - + +
142A LEU* 3.4 19.1 - - + +
144A ARG* 1.3 78.7 - - - +
146A ARG* 1.3 63.4 + - + +
147A GLU* 3.5 4.9 + - - +
91B ALA* 4.6 5.4 + - - +
92B GLU* 3.9 32.9 - - + +
95B VAL* 3.6 43.5 - - + +
1150B ACT 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 3.9 1.8 - - - +
120A GLU* 3.0 40.4 + - - -
142A LEU* 3.2 36.0 + - - +
143A HIS* 3.7 20.9 + - - +
144A ARG 3.1 1.0 - - - -
145A TYR* 1.3 78.8 - - + +
147A GLU* 1.3 65.4 + - - +
92B GLU* 2.6 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 3.4 12.4 + - - +
144A ARG* 2.9 35.6 + - - +
145A TYR 4.0 5.7 - - - +
146A ARG* 1.3 82.9 - - - +
----------------------------------------------------------
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