Contacts of the helix formed by residues 16 - 29 (chain A) 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 GLY 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ALA 3.2 3.4 + - - -
15A THR* 1.3 78.5 - - - +
17A LYS* 1.3 65.5 + - - +
18A THR 3.2 3.1 + - - -
19A THR* 3.4 9.5 + - - -
20A LEU* 3.0 25.5 + - - +
110A CYS* 4.1 4.3 - - - -
120A ARG* 5.0 2.7 - - - -
124A ARG* 5.4 2.5 - - - -
166A THR* 4.6 8.0 - - - +
193A CL 3.2 12.1 - - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.8 17.5 - - + +
10A THR 4.1 4.9 - - - +
11A GLY 3.1 31.0 - - - +
12A HIS 3.8 10.8 - - - -
13A PRO* 4.3 9.8 - - - +
14A ALA 5.3 0.8 - - - +
15A THR* 3.4 9.4 - - - +
16A GLY* 1.3 78.2 - - - +
18A THR* 1.3 63.4 + - - +
20A LEU* 4.5 0.4 - - - -
21A SER* 2.9 33.4 + - - -
36A ASP* 3.9 17.4 + - - -
82A GLU* 2.7 31.2 + - + +
83A SER* 3.8 10.7 - - - +
84A ASN* 4.0 16.4 + - - +
110A CYS* 3.7 16.9 - - - -
193A CL 3.5 4.5 - - + +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.2 0.6 - - - -
17A LYS* 1.3 83.8 + - - +
19A THR* 1.3 68.0 + - - +
21A SER* 2.9 20.2 + - - +
22A GLN* 3.0 41.3 + - - +
34A SER* 5.7 1.8 - - - +
36A ASP* 5.0 5.0 + - - +
82A GLU* 4.3 14.1 + - - +
124A ARG* 5.2 2.9 + - - -
193A CL 3.3 17.5 - - - +
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.4 11.3 + - - -
18A THR* 1.3 78.9 - - - +
20A LEU* 1.3 57.8 + - - +
22A GLN* 3.3 13.0 + - - +
23A ALA* 3.0 26.9 + - + +
124A ARG* 5.8 2.1 + - - -
174A MSE 4.6 13.2 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.3 6.3 - - + -
16A GLY 3.0 17.3 + - - +
17A LYS 4.1 1.8 - - - +
19A THR* 1.3 78.6 - - - +
21A SER* 1.3 57.7 + - - +
23A ALA* 3.2 3.1 + - - +
24A LEU* 2.9 51.0 + - + +
108A ILE* 3.9 19.1 - - + -
110A CYS* 3.8 20.0 - - - -
164A VAL* 4.1 18.8 - - + -
166A THR* 5.3 4.0 - - + -
172A ILE* 5.7 1.1 - - + -
174A MSE 4.0 24.9 - - + +
177A ILE* 4.0 25.1 - - + -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.1 17.2 - - - +
17A LYS 2.9 18.3 + - - -
18A THR* 2.9 19.9 + - - +
20A LEU* 1.3 76.6 - - - +
22A GLN* 1.3 56.6 + - - +
24A LEU* 3.3 7.9 + - - +
25A ALA* 2.9 29.5 + - - +
32A LEU* 3.7 26.1 - - - +
80A ILE* 4.2 3.6 - - - +
82A GLU* 3.7 21.7 + - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 3.0 42.6 + - + +
19A THR* 3.7 11.5 + - - +
21A SER* 1.3 78.9 + - - +
23A ALA* 1.3 56.3 + - - +
25A ALA* 3.3 2.4 + - - +
26A THR* 3.0 31.8 + - - +
32A LEU* 3.8 22.2 - - + +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.0 15.3 + - + +
20A LEU 3.5 7.6 - - - +
22A GLN* 1.3 72.8 - - - +
24A LEU* 1.3 61.4 + - - +
26A THR* 3.3 11.2 - - + +
27A GLY* 2.8 28.6 + - - -
174A MSE 3.6 36.6 - - + -
178A VAL* 4.2 6.9 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.3 11.2 - - + -
9A VAL* 3.9 19.3 - - + -
20A LEU* 2.9 28.3 + - + +
21A SER 3.6 7.6 - - - +
23A ALA* 1.3 77.9 - - + +
25A ALA* 1.3 56.7 + - - +
28A LEU* 2.8 45.3 + - + +
80A ILE* 3.7 11.4 - - + +
108A ILE* 3.5 24.7 - - + -
174A MSE 5.8 1.3 - - - -
177A ILE* 4.3 7.0 - - + -
178A VAL* 4.0 34.3 - - + +
181A VAL* 4.0 15.3 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER 2.9 17.0 + - - +
22A GLN* 3.7 4.3 - - - +
23A ALA 3.3 0.2 - - - -
24A LEU* 1.3 75.5 - - - +
26A THR* 1.3 54.2 + - - +
29A ARG* 2.8 30.0 + - - -
30A LEU 3.0 25.2 + - - +
32A LEU* 3.9 20.9 - - + -
80A ILE* 3.3 16.1 - - + +
71B THR* 5.7 0.2 - - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN 3.0 20.9 + - - +
23A ALA* 3.3 12.8 - - - +
25A ALA* 1.3 79.9 - - - +
27A GLY* 1.3 65.2 + - - +
29A ARG* 3.6 9.5 + - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 2.8 23.9 + - - -
26A THR* 1.3 77.5 - - - +
28A LEU* 1.3 62.7 + - - +
178A VAL* 4.4 18.3 - - - +
182A ARG* 4.6 5.7 + - - -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.9 17.9 - - + -
24A LEU* 2.8 30.4 + - + +
27A GLY* 1.3 75.8 - - - +
29A ARG* 1.3 72.0 + - - +
30A LEU* 4.0 20.2 - - + +
80A ILE* 4.9 0.4 - - + -
178A VAL* 3.8 22.4 - - + +
181A VAL* 3.8 27.4 - - + -
182A ARG* 3.7 51.8 + - + +
185A LEU* 4.3 9.2 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 2.8 13.2 + - - -
26A THR* 3.6 7.3 + - - +
27A GLY 3.5 2.2 - - - -
28A LEU* 1.3 82.0 - - - +
30A LEU* 1.3 63.6 + - - +
77A GLN* 4.5 0.7 + - - -
0B GLY 2.9 33.1 + - - +
1B MSE 5.0 3.8 + - - +
2B GLN 4.3 10.3 + - - -
4B PRO* 5.4 2.4 - - - +
73B LEU 5.2 0.6 + - - -
74B GLN 3.8 19.7 + - - +
75B SER* 3.5 36.3 + - - +
76B GLY* 3.4 21.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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