Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 1TW2
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 1.3 78.6 - - - +
16A LEU* 1.3 62.6 + - - +
17A ARG 3.2 0.4 - - - -
18A THR* 3.4 28.0 - - - +
19A LEU 3.4 15.4 + - - -
90B VAL* 3.9 28.4 - - + +
93B LEU* 4.1 6.7 - - - +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 4.0 16.0 - - + +
15A ALA* 1.3 75.0 - - - +
17A ARG* 1.3 63.2 + - + +
18A THR 3.3 0.4 - - - -
19A LEU* 3.7 3.5 + - - +
20A ILE* 3.1 53.8 + - + +
93B LEU* 3.5 26.6 - - + +
98B HIS* 6.0 0.9 - - + -
100B ALA* 4.3 23.3 - - + -
102B GLN* 4.4 11.2 - - + +
338B THR* 6.3 3.8 - - + -
1600B ERT 6.3 2.5 - - + -
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 2.8 36.6 + - - +
15A ALA 3.2 0.2 - - - -
16A LEU* 1.3 82.0 - - + +
18A THR* 1.3 55.2 + - - +
20A ILE* 4.0 11.4 - - + +
21A ARG* 2.7 56.9 + - + +
295B GLN* 4.3 27.4 - - - +
338B THR 4.3 11.3 + - - -
339B ILE* 4.9 0.4 - - - +
340B PRO* 3.5 35.3 - - - +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP 4.3 2.6 + - - -
15A ALA* 3.4 29.0 - - + +
16A LEU 3.3 0.2 - - - -
17A ARG* 1.3 80.1 - - - +
19A LEU* 1.3 61.2 + - - +
21A ARG* 3.6 9.8 + - - +
22A LEU* 3.2 34.6 + - + +
90B VAL* 4.4 17.7 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 3.4 9.7 + - - +
16A LEU* 4.0 9.0 - - - +
17A ARG 3.4 0.2 - - - -
18A THR* 1.3 78.0 - - - +
20A ILE* 1.3 59.9 + - + +
22A LEU* 3.3 3.5 + - + +
23A GLY* 3.0 25.6 + - - -
31B VAL* 4.2 14.8 - - + -
76B LEU* 3.8 36.3 - - + -
90B VAL* 4.3 11.8 - - + +
93B LEU* 3.8 22.7 - - + -
94B LEU* 4.0 18.8 - - + -
102B GLN* 3.6 33.0 - - + -
106B HIS* 4.2 5.6 - - + +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.1 40.2 + - + +
17A ARG* 3.6 11.6 + - + +
18A THR 3.4 0.2 - - - -
19A LEU* 1.3 76.1 - - - +
21A ARG* 1.3 64.3 + - + +
23A GLY 3.4 2.6 + - - -
24A SER* 3.1 23.3 + - - -
102B GLN* 3.9 24.2 - - + +
106B HIS* 4.7 8.4 - - + +
298B GLU* 3.3 33.9 - - - +
1600B ERT 4.9 20.0 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 2.7 41.7 + - + +
18A THR* 3.7 8.5 - - - +
20A ILE* 1.3 77.7 - - + +
22A LEU* 1.3 63.8 + - + +
24A SER* 3.3 19.6 + - - +
27A THR* 5.8 0.5 - - - -
294B GLU* 3.8 37.4 + - - +
295B GLN* 5.1 4.2 - - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 3.2 30.3 + - + +
19A LEU* 3.3 6.7 + - + +
21A ARG* 1.3 80.9 - - + +
23A GLY* 1.3 57.9 + - - +
24A SER 3.3 1.7 + - - +
21B ARG* 4.1 25.1 - - - +
27B THR* 3.8 24.1 - - + +
28B PRO* 3.3 24.1 - - - +
31B VAL* 4.1 12.6 - - + -
74B ILE* 3.6 30.1 - - + +
76B LEU* 3.6 29.8 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU 3.0 10.5 + - - -
20A ILE 3.6 3.6 - - - -
21A ARG 3.3 0.4 - - - -
22A LEU* 1.3 75.8 - - - +
24A SER* 1.3 52.2 + - - +
28B PRO* 3.6 12.3 - - - -
31B VAL* 4.1 9.1 - - - +
32B ARG* 2.7 40.4 + - - -
106B HIS* 3.7 22.6 - - - -
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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