Contacts of the strand formed by residues 45 - 53 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ALA* 5.5 1.3 - - - -
14M LEU* 6.2 0.2 - - + -
24M VAL* 3.9 33.0 - - + -
36M LEU* 4.2 14.8 - - + -
38M SER* 3.3 7.0 - - - +
39M TYR* 3.6 22.4 - - + -
43M MET* 3.2 22.9 - - - +
44M ASN* 1.3 79.2 - - - +
46M VAL* 1.3 65.3 + - - +
47M LEU* 4.3 1.6 - - + -
66M VAL* 3.3 7.3 - - - +
67M ILE* 2.7 49.9 + - + +
72M VAL* 4.3 6.3 - - + -
75M ILE* 3.7 31.6 - - + -
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Residues in contact with VAL 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L THR* 4.6 2.5 - - + -
10L ALA* 3.4 41.1 - - + +
13L VAL* 4.1 18.4 - - + -
36M LEU* 3.8 1.0 - - - +
37M ARG* 2.8 41.6 + - + -
38M SER* 3.1 19.7 + - - +
45M LEU* 1.3 77.9 - - - +
47M LEU* 1.3 76.2 + - - +
48M SER* 5.6 0.2 - - - -
64M THR* 4.2 7.0 - - + -
65M ILE 3.2 9.0 - - - +
66M VAL* 4.2 13.7 - - + -
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Residues in contact with LEU 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M VAL* 3.7 24.9 - - + -
24M VAL* 4.1 12.8 - - + -
32M VAL* 3.9 27.8 - - + -
33M ARG 4.0 3.6 - - - -
34M GLY* 3.9 21.3 - - - +
35M MET 3.1 7.6 - - - +
36M LEU* 3.8 19.3 - - + +
45M LEU* 4.8 2.7 - - + -
46M VAL* 1.3 85.8 - - - +
48M SER* 1.3 60.0 + - - +
50M SER* 4.0 5.8 - - - -
63M GLY 3.6 1.9 - - - +
64M THR* 3.3 4.0 - - - +
65M ILE* 2.9 43.7 + - + +
67M ILE* 4.0 15.3 - - + -
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Residues in contact with SER 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M GLY* 3.7 0.2 - - - -
35M MET* 2.9 34.3 + - - +
37M ARG* 2.8 40.2 + - - +
46M VAL* 5.7 0.2 - - - -
47M LEU* 1.3 73.6 - - - +
49M ASP* 1.3 76.6 + - - +
50M SER 2.9 4.1 + - - -
63M GLY 3.7 2.0 - - - -
64M THR* 3.9 15.9 - - - -
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Residues in contact with ASP 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU* 6.0 0.9 - - - +
33M ARG 4.4 0.3 - - - +
34M GLY* 4.2 6.1 - - - -
35M MET* 4.8 11.2 - - + +
37M ARG* 5.3 3.3 + - - -
48M SER* 1.3 79.8 + - - +
50M SER* 1.3 62.8 + - - +
51M GLU* 5.3 1.4 - - - +
63M GLY* 3.2 15.6 + - - -
64M THR* 4.7 0.8 + - - -
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Residues in contact with SER 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ARG 3.0 15.3 - - - -
47M LEU* 4.0 15.3 - - - -
48M SER 2.9 1.3 + - - -
49M ASP* 1.3 80.3 - - - +
51M GLU* 1.3 64.0 + - - +
61M LYS* 3.6 4.7 - - - +
62M LEU* 2.8 32.4 + - - +
63M GLY 2.7 23.9 + - - -
65M ILE* 3.4 31.4 - - - +
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Residues in contact with GLU 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M VAL* 3.2 5.9 - - - +
33M ARG* 2.9 55.0 + - + +
49M ASP 5.3 1.1 - - - +
50M SER* 1.3 76.0 - - - +
52M GLU* 1.3 58.9 + - - +
53M ILE* 3.8 24.1 + - + +
59M GLY* 3.4 16.5 - - - -
60M LYS 3.1 20.2 - - - +
61M LYS* 4.3 5.4 - - + +
62M LEU* 4.2 6.1 - - - +
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Residues in contact with GLU 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L LYS* 2.6 30.4 + - - +
30M LYS* 3.7 26.9 + - + +
31M GLU 3.9 7.6 - - - +
32M VAL* 4.2 7.6 - - + +
51M GLU* 1.3 72.5 - - - +
53M ILE* 1.3 66.6 - - - +
54M GLN* 3.0 24.2 + - - +
59M GLY* 3.5 0.7 - - - -
60M LYS* 2.8 53.3 + - + +
62M LEU* 3.7 18.8 - - + +
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Residues in contact with ILE 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LYS* 5.1 7.4 - - - -
31M GLU* 3.0 38.6 + - + +
32M VAL* 4.5 0.7 - - - -
33M ARG* 3.6 55.6 - - + +
51M GLU* 3.8 25.8 - - + +
52M GLU* 1.3 77.5 - - - +
54M GLN* 1.3 76.4 + - - +
57M GLY* 3.8 20.6 - - - +
58M SER 3.5 1.6 - - - +
59M GLY* 4.4 5.4 - - - -
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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