Contacts of the helix formed by residues 138 - 146 (chain H) in PDB entry 3HR4
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 138 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H GLU* 3.5 24.8 + - - +
85H ILE* 3.7 24.1 - - + +
86H ARG* 3.2 39.1 + - + +
89H PHE* 3.8 14.8 - + + -
98H GLY 4.4 1.2 + - - +
137H ASN* 1.3 85.8 + - - +
139H GLU* 1.3 55.4 + - - +
141H PHE* 3.4 17.5 - + + -
142H VAL* 2.5 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ASN* 2.1 28.8 + - - +
138H TYR* 1.3 65.6 - - - +
140H GLU* 1.3 67.2 + - + +
141H PHE 2.9 1.5 + - - -
142H VAL* 3.1 16.3 + - - +
143H GLN* 3.4 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H ALA* 3.3 20.3 - - - +
129H ASP* 2.7 29.3 - - - +
130H ILE* 2.9 29.2 + - + +
131H ASP* 3.0 15.6 + - - +
136H VAL* 3.4 24.8 - - + +
137H ASN* 2.9 16.3 + - - +
139H GLU* 1.3 78.6 - - + +
141H PHE* 1.3 59.4 + - - +
143H GLN* 4.0 7.0 + - - +
144H MET* 3.3 20.3 + - - +
204H CA 2.9 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515G LEU* 5.6 4.5 - - + -
519G VAL* 3.4 37.5 - - + -
85H ILE* 3.9 17.3 - - + -
88H ALA 3.9 12.8 - - - -
89H PHE* 3.2 49.4 - + + -
92H PHE* 3.9 14.1 - + - -
100H ILE* 6.4 1.1 - - + -
136H VAL* 4.2 8.5 - - + +
137H ASN 2.9 21.8 + - - +
138H TYR* 3.2 16.8 - + - +
139H GLU 2.9 0.2 - - - -
140H GLU* 1.3 79.0 - - - +
142H VAL* 1.3 66.8 + - - +
144H MET* 2.8 31.0 + - + +
145H MET* 3.5 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ILE* 4.4 9.7 - - - +
138H TYR* 2.5 37.1 + - + +
139H GLU* 3.1 8.9 + - - +
141H PHE* 1.3 74.0 - - - +
143H GLN* 1.3 65.1 + - + +
145H MET* 3.2 17.3 + - - +
146H THR* 3.6 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H GLU* 3.4 23.1 + - - +
140H GLU* 4.5 5.5 - - - +
141H PHE 3.3 0.4 - - - -
142H VAL* 1.3 75.0 - - + +
144H MET* 1.3 62.5 + - - +
145H MET* 2.9 8.4 + - - +
146H THR* 3.4 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515G LEU* 3.9 29.4 - - - -
516G LYS* 3.2 46.9 - - + +
519G VAL* 4.2 17.0 - - + -
127H GLU 5.0 2.9 - - - +
128H ALA* 3.8 26.2 - - + -
136H VAL* 6.1 0.4 - - + -
140H GLU 3.3 16.2 + - - +
141H PHE* 2.8 28.6 + - + +
143H GLN* 1.3 76.6 - - - +
145H MET* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G LYS* 5.3 1.3 - - - -
519G VAL* 3.3 50.5 - - + +
520G LYS* 4.0 21.4 - - + +
523G LEU* 3.3 34.3 - - + -
76H MET* 4.3 12.8 - - + -
85H ILE* 3.5 36.1 - - + -
141H PHE* 4.0 9.6 - - + +
142H VAL 3.2 2.4 + - - +
143H GLN 2.9 2.6 - - - +
144H MET* 1.3 88.1 - - + +
146H THR* 1.3 71.9 + - + +
147H ALA* 3.3 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H MET* 5.8 3.5 - - + +
81H SER* 5.8 3.4 - - - +
85H ILE* 4.5 16.8 - - + -
142H VAL 3.6 12.1 + - - -
143H GLN* 3.4 15.6 - - - +
145H MET* 1.3 83.0 - - + +
147H ALA* 1.3 62.2 + - - +
----------------------------------------------------------
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