Contacts of the strand formed by residues 45 - 53 (chain C) in PDB entry 1TH7
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 LEU 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 5.6 1.1 - - - -
24C VAL* 3.9 36.3 - - + -
36C LEU* 4.0 15.0 - - + -
38C SER* 3.3 7.0 - - - +
39C TYR* 3.6 22.9 - - + -
43C MET* 3.2 20.2 - - - +
44C ASN* 1.3 82.4 - - - +
46C VAL* 1.3 66.3 + - - +
47C LEU* 4.3 1.3 - - + -
66C VAL* 3.3 7.1 - - - +
67C ILE* 2.7 49.4 + - + +
72C VAL* 4.3 5.6 - - + -
75C ILE* 3.9 27.6 - - + -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 4.7 2.5 - - + -
10B ALA* 3.5 37.9 - - + +
13B VAL* 4.1 18.8 - - + -
36C LEU* 3.6 1.4 - - - +
37C ARG* 2.8 41.8 + - + -
38C SER* 3.1 19.3 + - - +
45C LEU* 1.3 80.7 - - - +
47C LEU* 1.3 69.8 + - - +
64C THR* 4.2 11.4 - - + -
65C ILE 3.3 9.0 - - - +
66C VAL* 4.2 14.1 - - + -
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Residues in contact with LEU 47 (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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22C VAL* 3.7 24.9 - - + -
24C VAL* 4.0 12.6 - - + -
32C VAL* 3.8 28.7 - - + -
33C ARG 4.2 2.7 - - - +
34C GLY* 4.0 21.3 - - - +
35C MET 3.1 4.9 - - - +
36C LEU* 3.8 19.7 - - + +
45C LEU* 4.8 2.5 - - + -
46C VAL* 1.3 87.1 - - - +
48C SER* 1.3 60.4 + - - +
50C SER* 4.1 6.3 - - - -
63C GLY 3.6 1.9 - - - +
64C THR* 3.3 4.2 - - - +
65C ILE* 2.9 43.1 + - + -
67C ILE* 3.9 16.8 - - + -
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Residues in contact with SER 48 (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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34C GLY* 3.7 0.2 - - - -
35C MET* 2.8 35.0 + - - +
37C ARG* 2.9 40.6 + - - +
46C VAL* 5.7 0.2 - - - -
47C LEU* 1.3 72.6 - - - +
49C ASP* 1.3 77.1 + - - +
50C SER 3.0 3.6 + - - -
63C GLY 3.9 2.5 - - - -
64C THR* 4.0 15.0 - - - -
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Residues in contact with ASP 49 (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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33C ARG 4.2 0.3 - - - +
34C GLY* 4.1 6.1 - - - -
35C MET* 4.9 11.4 - - + +
37C ARG* 5.3 3.6 + - - -
48C SER* 1.3 80.0 + - - +
50C SER* 1.3 63.7 + - - +
51C GLU* 4.4 7.5 - - - +
63C GLY* 3.3 15.4 + - - -
64C THR* 4.5 1.2 + - - +
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Residues in contact with SER 50 (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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32C VAL* 5.4 0.2 - - - -
33C ARG 3.0 14.6 - - - -
47C LEU* 4.1 17.0 - - - -
48C SER 3.0 1.3 + - - -
49C ASP* 1.3 78.0 - - - +
51C GLU* 1.3 70.4 + - - +
61C LYS* 3.5 2.9 - - - +
62C LEU* 2.9 36.5 + - - +
63C GLY 2.7 24.3 + - - -
65C ILE* 3.6 24.8 - - - +
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Residues in contact with GLU 51 (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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32C VAL* 3.3 5.7 - - - +
33C ARG* 2.8 63.1 + - - +
49C ASP 4.4 6.9 - - - +
50C SER* 1.3 81.9 - - - +
52C GLU* 1.3 60.8 + - - +
53C ILE* 3.7 2.8 + - + +
59C GLY* 3.8 21.9 - - - -
60C LYS 3.2 11.0 - - - +
61C LYS* 4.1 29.4 - - + +
62C LEU* 4.3 3.6 - - - +
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Residues in contact with GLU 52 (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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25B LYS* 3.3 26.1 + - - -
31B GLU* 5.5 1.4 - - - +
29C ASN* 4.0 0.7 - - - +
30C LYS* 3.4 49.0 + - + +
31C GLU 3.7 4.9 - - - +
32C VAL* 4.3 7.4 - - + -
51C GLU* 1.3 72.5 - - - +
53C ILE* 1.3 52.6 + - - +
54C GLN* 2.6 32.4 + - - +
59C GLY* 3.3 2.1 - - - -
60C LYS* 2.7 49.9 + - + +
62C LEU* 4.1 16.1 - - + +
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Residues in contact with ILE 53 (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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23C LEU* 4.5 7.0 - - + -
30C LYS* 3.3 24.6 - - - +
31C GLU* 2.9 43.4 + - + +
33C ARG* 3.9 48.5 - - + +
51C GLU* 4.4 4.9 - - + +
52C GLU* 1.3 75.5 - - - +
54C GLN* 1.3 72.4 + - - +
57C GLY* 4.4 10.8 - - - +
58C SER 3.7 10.5 - - - +
59C GLY* 4.7 2.2 - - - -
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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