Contacts of the helix formed by residues 86 - 101 (chain D) in PDB entry 2RHM
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 ARG 86 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASN* 4.1 8.3 - - - +
85D PHE* 1.3 76.4 - - - +
87D VAL* 1.3 60.4 + - - +
88D ASP* 2.8 44.3 + - - +
89D LEU* 4.1 20.1 - - + +
90D ASP* 2.8 44.4 + - - +
93D ARG* 6.1 0.4 - - - +
155D LEU* 3.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE 4.2 0.8 + - - -
86D ARG* 1.3 71.5 - - - +
88D ASP* 1.3 62.9 + - - +
89D LEU 3.3 0.9 + - - -
91D THR* 2.7 38.5 + - - +
153D PRO* 4.0 24.7 - - + +
154D PRO 3.3 27.6 - - - +
155D LEU* 3.9 4.6 - - + +
156D PRO* 4.0 16.6 - - + -
195D GOL 5.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG* 2.8 48.1 + - - +
87D VAL* 1.3 80.1 - - - +
89D LEU* 1.3 78.9 + - - +
91D THR* 5.7 0.2 - - - -
92D GLU* 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG* 3.3 21.9 + - + +
88D ASP* 1.3 103.8 + - - +
90D ASP* 1.3 64.9 + - - +
91D THR 3.4 2.4 + - - -
92D GLU* 3.7 8.5 + - - +
93D ARG* 3.4 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 4.2 5.8 - - - +
66D TYR* 2.9 27.2 + - - +
85D PHE* 3.4 17.0 - - - -
86D ARG* 2.8 44.4 + - - +
89D LEU* 1.3 70.1 - - - +
91D THR* 1.3 65.7 + - - +
93D ARG* 2.9 28.9 + - - -
94D MSE 2.9 28.6 + - - +
155D LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG 4.0 0.4 + - - -
87D VAL* 2.7 29.6 + - + +
89D LEU 3.4 0.8 - - - -
90D ASP* 1.3 78.4 - - - +
92D GLU* 1.3 61.9 + - - +
94D MSE 3.3 5.0 + - - +
95D GLN* 3.1 47.3 + - + +
155D LEU* 4.4 2.0 - - - +
156D PRO* 3.3 45.6 - - + +
157D LEU* 4.8 8.4 - - + +
195D GOL 4.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASP 5.9 1.7 - - - +
89D LEU* 3.7 9.2 + - - +
90D ASP 3.3 0.4 - - - -
91D THR* 1.3 79.3 - - - +
93D ARG* 1.3 59.7 + - + +
95D GLN* 3.2 12.4 + - - +
96D ASN* 2.8 45.6 + - - +
195D GOL 3.6 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ALA* 5.9 4.6 + - - +
62D ILE* 3.4 24.2 - - - +
66D TYR* 3.5 35.4 - - + +
86D ARG* 6.1 0.2 - - - +
89D LEU* 3.4 47.7 + - - +
90D ASP* 2.9 35.7 + - - +
91D THR 3.3 0.4 - - - -
92D GLU* 1.3 77.8 - - + +
94D MSE 1.3 57.4 + - - +
96D ASN* 3.3 10.4 + - - +
97D LEU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.7 24.0 - - - -
8D ILE* 4.0 17.0 - - + -
66D TYR* 3.4 24.7 - - + +
81D MSE 3.7 27.4 - - + -
85D PHE* 3.9 12.3 - - + -
90D ASP 2.9 20.7 + - - +
91D THR 3.7 0.9 - - - +
93D ARG* 1.3 73.0 - - - +
95D GLN* 1.3 60.6 + - - +
97D LEU* 3.3 5.0 + - - +
98D HIS* 2.9 29.9 + - - +
103D PHE* 3.6 12.5 - - + -
155D LEU* 4.2 11.2 - - + -
157D LEU* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR* 3.1 32.0 + - + +
92D GLU* 3.4 10.5 - - + +
94D MSE 1.3 76.8 - - + +
96D ASN* 1.3 65.9 + - - +
98D HIS* 3.3 8.4 + - - +
99D THR* 3.2 24.9 + - - -
156D PRO 5.4 2.0 + - - -
157D LEU* 5.8 3.1 - - + -
195D GOL 2.6 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU* 2.8 39.8 + - - +
93D ARG* 3.7 9.1 - - - +
94D MSE 3.3 0.2 - - - -
95D GLN* 1.3 76.1 - - - +
97D LEU* 1.3 65.5 + - - +
99D THR* 3.2 20.1 + - - -
100D ILE* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.9 28.0 - - + -
66D TYR* 3.8 34.5 - - + +
69D ALA* 4.1 9.4 - - + -
70D ALA* 3.7 37.7 - - + +
73D LEU* 4.0 8.7 - - + -
81D MSE 4.6 0.9 - - - -
93D ARG 2.9 17.4 + - - +
94D MSE 3.6 5.8 - - - +
96D ASN* 1.3 74.8 - - - +
98D HIS* 1.3 54.5 + - - +
100D ILE* 3.1 11.6 + - + +
101D ALA* 2.7 38.4 + - + +
103D PHE* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D THR* 5.6 0.6 - - - +
94D MSE 2.9 16.8 + - - +
95D GLN* 3.6 7.9 - - - +
96D ASN 3.2 0.2 - - - -
97D LEU* 1.3 76.8 - - - +
99D THR* 1.3 63.2 + - - +
101D ALA 3.7 2.5 - - - -
102D PRO* 3.2 32.2 - - + +
103D PHE* 3.1 59.4 + + + -
105D PRO* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN 3.2 13.9 + - - -
96D ASN* 3.5 12.7 + - - -
97D LEU 3.2 0.4 - - - -
98D HIS* 1.3 80.2 + - - +
100D ILE* 1.3 65.1 + - + +
102D PRO* 4.8 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA* 4.1 20.0 - - + -
74D GLN* 2.9 31.8 + - - +
96D ASN 3.5 11.4 + - - +
97D LEU* 3.4 14.8 - - + +
99D THR* 1.3 86.9 - - + +
101D ALA* 1.3 62.5 - - + +
102D PRO* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA* 3.9 20.6 - - - +
73D LEU* 3.9 15.9 - - + +
74D GLN* 3.8 21.1 - - + +
97D LEU* 2.7 20.3 + - + +
98D HIS 3.5 2.7 - - - -
100D ILE* 1.3 77.0 - - + +
102D PRO* 1.3 72.7 - - - +
103D PHE* 3.3 18.2 - - - -
----------------------------------------------------------
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