Contacts of the helix formed by residues 16 - 29 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 3.8 17.7 - - - +
14C ALA 3.1 3.4 + - - -
15C THR* 1.3 78.5 - - - +
17C LYS* 1.3 64.7 + - - +
18C THR 3.1 3.2 + - - -
19C THR* 3.3 6.5 + - - -
20C LEU* 3.0 25.4 + - - +
110C CYS* 4.2 3.4 - - - -
120C ARG* 4.9 2.7 - - - -
124C ARG* 4.9 4.5 - - - -
166C THR* 4.7 0.7 - - - -
193C CL 3.0 12.7 - - - +
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.8 18.1 - - + +
10C THR 4.1 3.4 - - - +
11C GLY 3.2 32.3 - - - +
12C HIS 3.8 10.5 - - - -
13C PRO* 4.4 8.8 - - - +
14C ALA 5.5 0.4 - - - +
15C THR* 3.5 9.4 - - - +
16C GLY* 1.3 77.6 - - - +
18C THR* 1.3 63.7 + - - +
20C LEU* 4.3 0.7 - - - -
21C SER* 2.8 33.6 + - - -
36C ASP* 4.7 12.1 + - - -
82C GLU* 2.8 32.2 + - + +
83C SER* 3.7 12.1 - - - +
84C ASN* 3.9 18.3 + - - +
110C CYS* 3.6 19.3 - - - -
193C CL 3.4 4.5 - - + +
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY 3.1 0.6 - - - -
17C LYS* 1.3 85.3 + - - +
19C THR* 1.3 64.6 + - - +
21C SER* 2.8 20.8 + - - +
22C GLN* 3.1 37.1 + - + +
34C SER* 5.8 1.6 - - - +
36C ASP* 5.5 2.8 + - - +
82C GLU* 4.2 15.0 + - - +
124C ARG* 5.2 2.1 + - - -
193C CL 3.4 17.5 - - - +
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.2 31.8 - - + +
16C GLY* 3.3 10.2 + - - -
18C THR* 1.3 79.5 - - - +
20C LEU* 1.3 59.0 + - - +
22C GLN* 3.3 12.9 + - + +
23C ALA* 3.0 28.3 + - + +
124C ARG* 5.5 4.3 + - - -
174C MSE 5.3 3.6 - - + -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.4 13.0 - - + +
9C VAL* 4.5 4.7 - - + -
16C GLY 3.0 18.0 + - - +
17C LYS* 4.0 4.7 - - - +
19C THR* 1.3 78.4 - - - +
21C SER* 1.3 62.0 + - - +
23C ALA* 3.3 4.3 + - - +
24C LEU* 3.0 43.5 + - + +
108C ILE* 4.0 18.6 - - + -
110C CYS* 3.9 19.1 - - - -
164C VAL* 4.0 30.5 - - + -
166C THR* 5.0 0.4 - - + -
174C MSE 4.2 20.1 - - + +
177C ILE* 4.3 13.0 - - + -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.1 17.5 - - - -
17C LYS 2.8 20.3 + - - -
18C THR* 2.8 20.6 + - - +
20C LEU* 1.3 73.9 - - - +
22C GLN* 1.3 57.4 + - - +
24C LEU* 3.3 8.8 + - - +
25C ALA* 2.9 27.4 + - - +
32C LEU* 3.9 18.9 - - - +
34C SER* 5.8 0.2 - - - -
80C ILE* 3.9 5.0 - - - +
82C GLU* 3.7 28.8 + - - +
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 3.1 38.3 + - + +
19C THR* 3.6 13.5 - - - +
20C LEU 3.3 0.2 - - - -
21C SER* 1.3 74.3 + - - +
23C ALA* 1.3 63.4 + - - +
25C ALA* 3.3 3.4 + - - +
26C THR* 3.0 30.0 + - - +
32C LEU* 3.7 21.8 - - + +
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.8 20.7 + - - +
19C THR* 3.0 15.1 + - + +
20C LEU 3.5 8.1 - - - +
22C GLN* 1.3 75.3 - - - +
24C LEU* 1.3 57.3 + - - +
26C THR* 3.5 4.1 + - - -
27C GLY* 2.9 27.7 + - - -
174C MSE 3.7 35.4 - - + -
178C VAL* 4.5 5.1 - - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.5 9.4 - - + -
9C VAL* 3.9 16.8 - - + -
20C LEU* 3.0 30.6 + - + +
21C SER* 3.6 7.4 - - - +
23C ALA* 1.3 73.4 - - + +
25C ALA* 1.3 60.4 + - - +
27C GLY 4.5 0.2 - - - +
28C LEU* 2.8 46.8 + - + +
80C ILE* 3.8 11.0 - - + -
108C ILE* 3.5 26.5 - - + -
174C MSE 5.6 0.7 - - - -
177C ILE* 4.3 5.4 - - + +
178C VAL* 4.0 26.7 - - + +
181C VAL* 3.8 23.1 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER 2.9 16.8 + - - +
22C GLN 3.3 6.5 + - - +
24C LEU* 1.3 77.0 - - - +
26C THR* 1.3 58.2 + - - +
29C ARG* 2.8 24.3 + - - -
30C LEU 3.0 27.5 + - - +
32C LEU* 3.9 19.5 - - + -
80C ILE* 3.4 15.4 - - + +
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 3.2 28.6 - - + +
29B ARG* 5.8 4.7 - - - +
22C GLN 3.0 16.8 + - - -
23C ALA* 3.8 5.4 - - - -
25C ALA* 1.3 78.5 - - - +
27C GLY* 1.3 62.9 + - - +
29C ARG* 3.6 11.9 + - - +
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 4.2 19.3 - - - +
27B GLY* 5.4 1.0 - - - -
23C ALA 2.9 17.2 + - - -
24C LEU 3.9 0.2 - - - -
26C THR* 1.3 78.8 - - - +
28C LEU* 1.3 61.6 + - - +
29C ARG* 5.3 0.3 - - - +
178C VAL* 4.4 11.9 - - - -
182C ARG* 3.5 21.8 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.0 4.9 - - + -
24C LEU* 2.8 35.0 + - + +
27C GLY* 1.3 76.4 - - - +
29C ARG* 1.3 69.9 + - - +
30C LEU* 3.7 34.7 - - + +
80C ILE* 4.9 0.9 - - + -
178C VAL* 3.9 14.6 - - + +
181C VAL* 3.7 23.8 - - + -
182C ARG* 3.4 36.1 - - + +
185C LEU* 4.1 14.1 - - + -
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA 2.8 13.3 + - - -
26C THR* 3.6 7.8 + - - +
27C GLY 3.4 3.0 - - - +
28C LEU* 1.3 81.6 - - - +
30C LEU* 1.3 62.1 + - - +
77C GLN* 4.8 1.0 + - - -
2D GLN 4.4 18.4 + - - +
4D PRO* 5.5 2.0 - - - +
73D LEU 4.7 1.8 + - - -
74D GLN* 3.4 23.8 + - - +
75D SER* 3.4 24.2 + - - +
76D GLY* 3.5 31.1 - - - +
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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