Contacts of the strand formed by residues 24 - 33 (chain C) in PDB entry 4M75
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 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.1 3.1 - - - +
18B GLU* 3.7 2.8 + - - -
22B ASP* 3.7 12.9 + - - +
68B ARG* 3.3 52.0 - - - +
69B TYR* 3.5 24.6 + - - +
19C LYS* 4.6 0.3 - - - +
20C LEU* 3.2 35.0 + - + +
21C ARG 5.7 0.4 - - - -
22C GLY* 3.0 25.9 + - - +
23C ALA* 1.3 80.4 - - - +
25C THR* 1.3 69.0 + - - +
46C GLU* 4.0 3.7 + - + +
47C THR 3.8 5.8 - - - +
48C ILE* 3.7 26.4 - - + +
49C TYR* 5.7 0.9 - - - -
61C ARG* 2.6 36.9 - - - +
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Residues in contact with THR 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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17C TYR* 3.5 34.2 + - + +
18C ILE 3.5 8.0 + - - +
19C LYS* 3.8 19.9 - - - +
20C LEU* 4.6 1.1 - - - +
24C ARG* 1.3 82.4 + - - +
26C LEU* 1.3 64.4 + - - +
27C VAL* 5.5 1.8 - - + -
46C GLU* 3.3 2.8 - - - +
47C THR* 2.5 54.3 + - - +
49C TYR* 4.2 19.8 + - - +
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Residues in contact with LEU 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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69B TYR* 3.1 22.4 - - + +
17C TYR* 3.8 3.6 - - - -
18C ILE* 3.0 39.4 + - + +
20C LEU* 2.7 39.5 - - + -
25C THR* 1.3 74.8 - - - +
27C VAL* 1.3 69.6 + - - +
41C LEU* 3.6 15.7 - - + -
44C ALA* 4.5 7.2 - - + -
45C VAL 3.4 4.5 - - - +
46C GLU* 3.6 21.3 - - + +
66C VAL* 4.4 11.2 - - + -
68C ILE* 3.6 22.7 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 3.2 30.5 - - + +
16C VAL 3.8 11.9 - - - +
17C TYR* 4.4 17.0 - - + -
25C THR* 5.5 2.2 - - + -
26C LEU* 1.3 80.6 - - - +
28C GLY* 1.3 59.4 + - - +
41C LEU* 4.3 2.5 - - - -
44C ALA* 2.8 5.3 - - - +
45C VAL* 2.5 57.0 + - + +
79C PRO* 4.9 15.3 - - + -
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Residues in contact with GLY 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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15C ARG* 3.4 9.6 - - - -
16C VAL* 3.3 29.7 + - - +
27C VAL* 1.3 77.7 - - - +
29C THR* 1.3 66.7 + - - -
41C LEU* 3.9 9.1 - - - +
43C ASP 3.3 14.4 - - - -
44C ALA* 3.6 10.3 - - - -
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Residues in contact with THR 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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13C ASP* 3.5 38.1 - - - +
14C GLU* 3.6 9.9 - - - +
15C ARG* 3.3 17.5 + - - +
28C GLY* 1.3 72.1 - - - -
30C LEU* 1.3 62.5 + - - +
31C GLN* 4.0 11.0 - - - +
41C LEU* 3.1 8.1 - - - +
42C SER* 3.0 45.9 + - - +
43C ASP* 4.3 3.8 + - - +
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Residues in contact with LEU 30 (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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83B GLN* 3.7 1.0 + - - -
8C LEU* 4.0 22.9 - - + +
11C ASN 4.2 4.0 - - - +
12C LEU* 3.8 26.3 - - + +
13C ASP* 2.8 31.7 + - - +
14C GLU 3.1 16.5 + - - +
16C VAL* 3.9 20.6 - - + -
29C THR* 1.3 74.3 - - - +
31C GLN* 1.3 60.6 + - - +
32C ALA 3.6 15.0 - - - +
33C PHE* 4.5 14.4 - - + -
39C ILE* 3.2 39.0 - - + -
40C VAL 3.7 1.3 - - - -
41C LEU* 3.9 4.5 - - + -
76C ILE* 6.1 0.9 - - + -
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Residues in contact with GLN 31 (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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79B THR* 2.6 37.4 - - + +
82B LEU* 3.7 10.0 - - + -
83B GLN* 2.4 63.1 + - - +
86B THR* 3.4 0.7 - - - +
12C LEU* 4.0 2.6 - - - +
13C ASP* 4.7 1.6 + - - -
29C THR* 4.0 10.5 - - - +
30C LEU* 1.3 73.7 - - - +
32C ALA* 1.3 62.6 + - - +
40C VAL* 2.9 21.5 + - + +
41C LEU 4.4 0.4 - - - -
42C SER* 2.4 50.2 + - - +
65C MSE 4.5 4.9 - - - -
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Residues in contact with ALA 32 (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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2B LEU* 4.5 5.6 - - + -
3B PHE* 4.1 9.0 - - + -
82B LEU* 3.9 13.5 - - + -
86B THR* 3.6 19.7 - - + -
12C LEU* 4.7 1.3 - - - -
30C LEU* 3.6 3.1 - - - +
31C GLN* 1.3 81.3 - - - +
33C PHE* 1.3 66.9 + - - +
39C ILE* 3.5 6.4 - - - +
40C VAL* 3.1 42.5 + - + +
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Residues in contact with PHE 33 (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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2B LEU* 4.0 11.3 - - - +
3B PHE* 3.7 7.6 - - - -
86B THR* 3.9 22.6 + - - -
89B GLU* 5.6 1.9 - - - +
91B MSE 2.2 52.3 - - + +
5C LEU* 3.0 25.6 - - + -
8C LEU* 3.3 37.9 - - + -
9C LYS* 3.8 21.1 - - + -
12C LEU* 4.4 7.9 - - + -
30C LEU* 4.5 10.5 - - + -
32C ALA* 1.3 78.2 - - - +
34C ASP* 1.3 66.4 + - - +
37C SER* 5.7 0.7 - - - -
38C ASN 3.4 10.3 - - - +
39C ILE* 4.1 15.0 - - + -
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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