Contacts of the helix formed by residues 7 - 18 (chain L) 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 ALA 7 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PHE* 5.7 0.3 - - - -
6G LEU* 3.9 18.4 - - + +
3L MET* 5.6 0.8 - - + +
4L ASN* 3.0 26.7 + - + +
5L PHE 3.4 0.9 - - - -
6L LEU* 1.3 73.2 - - - +
8L GLU* 1.3 63.5 + - - +
9L THR 3.3 2.9 - - - -
10L ALA* 3.2 17.2 + - + +
11L HIS* 3.3 11.4 + - - +
38M SER* 3.9 17.3 - - - +
39M TYR 4.5 5.4 - - - +
40M ASP* 4.5 5.6 - - + +
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Residues in contact with GLU 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 4.7 20.6 - - + +
15A ALA* 5.5 6.2 - - - +
39A TYR* 4.8 7.2 + - - -
5L PHE 4.8 1.8 - - - +
6L LEU* 2.9 22.8 + - - +
7L ALA* 1.3 72.0 - - - +
9L THR* 1.3 57.7 + - - +
11L HIS* 3.3 8.1 + - - +
12L LYS* 2.8 32.5 + - - +
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Residues in contact with THR 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA 3.2 1.0 + - - -
8L GLU* 1.3 78.2 - - - +
10L ALA* 1.3 62.9 + - - +
12L LYS* 3.3 12.2 + - + +
13L VAL* 3.2 24.9 + - + +
37M ARG* 3.6 32.0 + - + +
38M SER* 3.7 16.6 - - - -
46M VAL* 4.6 6.5 - - + -
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Residues in contact with ALA 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L MET* 3.6 26.3 - - + +
7L ALA* 3.2 13.7 + - + +
9L THR* 1.3 78.2 - - - +
11L HIS* 1.3 64.8 + - - +
13L VAL* 3.3 12.8 + - - +
14L LEU* 3.4 10.7 + - - +
38M SER* 3.7 12.0 + - - +
44M ASN* 5.9 5.8 - - + +
45M LEU 5.4 2.5 - - - +
46M VAL* 3.4 25.6 - - + -
66M VAL* 4.6 3.8 - - + +
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Residues in contact with HIS 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.3 56.2 + + + -
6A LEU* 4.4 2.7 - - + +
8A GLU* 3.6 20.2 + - + +
11A HIS* 5.7 7.0 - + - -
3L MET* 4.1 8.0 - - - +
4L ASN 5.8 0.2 - - - +
5L PHE 5.3 4.7 - - - +
7L ALA 3.3 9.9 + - - +
8L GLU* 3.7 11.2 - - - +
9L THR 3.3 0.2 - - - -
10L ALA* 1.3 77.7 - - - +
12L LYS* 1.3 58.1 + - - +
14L LEU* 3.2 5.0 + - - +
15L ALA* 2.9 25.8 + - + +
39L TYR* 2.9 36.3 + + - -
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Residues in contact with LYS 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L GLU 2.8 18.0 + - - +
9L THR* 3.5 11.9 - - + +
11L HIS* 1.3 74.7 - - - +
13L VAL* 1.3 60.9 + - + +
15L ALA* 3.7 7.1 - - + +
16L GLU* 2.9 61.5 + - + +
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Residues in contact with VAL 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L THR* 3.2 17.6 + - + +
10L ALA 3.3 7.6 + - - +
12L LYS* 1.3 78.8 - - + +
14L LEU* 1.3 59.6 + - + +
16L GLU* 3.5 7.1 + - - +
17L SER* 2.7 33.0 + - - +
75L ILE* 6.5 0.4 - - + -
77L PRO* 3.9 23.7 - - + +
46M VAL* 4.1 24.7 - - + -
64M THR* 4.1 16.6 - - + -
66M VAL* 3.6 22.7 - - + -
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Residues in contact with LEU 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L MET* 3.7 33.4 - - + -
10L ALA 3.4 6.7 + - - +
11L HIS* 3.2 7.9 + - - +
13L VAL* 1.3 75.7 - - + +
15L ALA* 1.3 65.2 + - - +
17L SER* 3.1 14.0 + - - -
18L LEU 3.1 10.7 + - - -
36L LEU* 3.9 11.6 - - + +
39L TYR* 3.6 46.7 - - + -
40L ASP 4.8 2.0 - - - +
43L MET* 5.1 2.7 - - + -
75L ILE* 4.0 39.9 - - + -
66M VAL* 4.3 17.3 - - + -
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Residues in contact with ALA 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 5.0 6.3 - - - +
11L HIS* 2.9 22.3 + - + +
12L LYS* 3.7 9.4 - - + +
14L LEU* 1.3 76.8 - - - +
16L GLU* 1.3 61.5 + - + +
18L LEU* 3.4 20.6 - - - +
39L TYR* 3.6 19.8 + - - +
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Residues in contact with GLU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LYS* 2.9 55.9 + - + +
13L VAL* 4.0 6.3 - - - +
15L ALA* 1.3 78.7 - - + +
17L SER* 1.3 58.2 + - - +
18L LEU 3.3 1.2 - - - +
20L ASN* 3.0 21.3 + - - -
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Residues in contact with SER 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L VAL* 2.7 22.3 + - - +
14L LEU* 3.1 9.7 + - - +
16L GLU* 1.3 75.7 - - - +
18L LEU* 1.3 65.4 + - - +
19L ASN 3.3 0.2 + - - -
20L ASN* 2.9 29.9 + - - +
22L VAL* 3.9 19.5 - - - -
36L LEU* 3.7 11.4 - - - +
75L ILE* 5.9 0.9 - - - -
77L PRO* 2.9 31.1 - - - +
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Residues in contact with LEU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LEU 3.1 8.4 + - - +
15L ALA* 3.4 17.6 - - - +
16L GLU 3.3 2.4 - - - +
17L SER* 1.3 78.6 - - - +
19L ASN* 1.3 84.7 + - - +
20L ASN* 3.3 10.0 + - - -
36L LEU* 3.8 8.5 - - + +
37L ARG 3.6 33.0 - - - +
38L SER* 3.9 5.2 - - - +
39L TYR* 4.1 25.1 - - + -
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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