Contacts of the helix formed by residues 18 - 29 (chain B) in PDB entry 1TD2
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 GLY 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.8 15.7 - - - -
10B SER* 3.5 15.3 - - - -
17B ALA* 1.3 71.4 - - - +
19B ASN* 1.3 51.3 + - - -
21B ALA* 3.0 2.9 + - - +
22B ALA* 2.7 35.2 + - - +
224B ASP* 2.7 30.9 + - - +
289B PXL 3.9 3.2 - - - -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA* 3.1 44.3 + - - +
9B GLN* 3.3 28.6 + - - +
10B SER 2.9 16.0 + - - +
11B HIS* 4.9 3.4 - - + -
18B GLY* 1.3 68.9 - - - -
20B SER* 1.3 61.0 + - - +
22B ALA* 4.2 1.5 - - - +
23B GLU* 2.9 39.6 + - + +
26B MET* 6.0 0.2 - - - +
33B VAL* 4.8 2.8 - - - +
35B PRO* 3.7 15.3 - - + +
36B LEU 3.9 0.6 + - - -
37B ASN* 3.0 28.9 - - - +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.7 13.5 + - - +
35A PRO* 6.2 0.7 - - - -
10B SER 3.9 0.4 + - - -
11B HIS* 2.9 20.3 - - - -
12B VAL* 2.7 55.0 + - - -
15B GLY 4.0 5.4 - - - -
16B HIS* 2.8 23.3 + - - -
17B ALA 3.0 5.8 + - - -
19B ASN* 1.3 78.7 - - - +
21B ALA* 1.3 58.7 + - - +
23B GLU* 5.3 3.0 - - - +
24B PHE* 5.5 2.8 + - - +
268B VAL* 4.7 1.6 - - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 3.7 13.9 - - + +
17B ALA* 3.3 25.0 - - - +
18B GLY 3.0 7.8 + - - +
20B SER* 1.3 79.3 - - - +
22B ALA* 1.3 59.4 + - - +
23B GLU 3.7 0.4 - - - -
25B PRO* 3.0 28.6 - - - +
221B GLY* 4.4 11.7 - - - +
224B ASP* 4.7 1.1 - - + -
225B VAL* 3.9 17.9 - - + +
266B LEU* 4.9 3.1 - - + -
268B VAL* 3.8 7.6 - - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.8 17.9 - - - +
18B GLY 2.7 19.9 + - - +
19B ASN* 4.5 1.1 - - - +
21B ALA* 1.3 74.5 - - - +
23B GLU* 1.3 63.6 + - - +
25B PRO* 3.2 3.9 - - - +
26B MET* 3.1 39.4 + - + +
224B ASP 3.6 24.7 - - - +
225B VAL* 4.6 7.4 - - - +
228B GLY* 4.8 0.9 - - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.6 37.8 - - - +
24A PHE* 4.3 1.0 - - - -
27A ARG* 3.2 14.4 + - - -
19B ASN* 2.9 28.9 + - + +
20B SER* 5.3 1.2 - - - +
22B ALA* 1.3 71.8 - - - +
24B PHE* 1.3 80.8 + - - +
26B MET* 3.2 5.1 + - - +
27B ARG* 3.0 57.2 + - - +
33B VAL* 4.0 23.1 - - + +
35B PRO* 4.5 10.3 - - + -
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 4.1 3.1 - - - +
24A PHE* 3.5 34.1 - + - -
27A ARG* 3.6 40.8 - - + +
28A ARG* 4.0 6.3 - - - -
19B ASN 4.7 0.4 + - - -
20B SER 5.5 2.4 + - - +
21B ALA 4.6 0.4 + - - -
23B GLU* 1.3 90.4 + - - +
25B PRO* 1.4 77.7 - - + +
27B ARG* 2.9 5.6 + - - +
28B ARG* 2.8 40.1 + - + +
268B VAL* 3.8 26.0 - - + -
269B VAL* 4.0 9.9 - - + -
272B GLN* 3.6 40.8 - - + -
275B ILE* 5.2 0.7 - - + -
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 3.0 28.7 - - - +
22B ALA* 3.2 6.7 - - - +
24B PHE* 1.4 93.2 - - + +
26B MET* 1.3 59.6 + - - +
28B ARG* 3.3 7.5 + - + +
29B LEU* 3.2 19.4 + - - +
225B VAL* 4.3 13.5 - - + -
229B LEU* 3.7 22.8 - - + +
268B VAL* 3.8 23.3 - - + -
275B ILE* 3.9 26.6 - - + +
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.5 40.8 - - + -
7B ALA* 5.3 6.5 - - + -
9B GLN* 5.7 0.9 - - - -
19B ASN* 6.0 0.2 - - - +
22B ALA* 3.1 32.7 + - - +
23B GLU* 3.5 7.0 - - - +
24B PHE 3.1 0.2 - - - -
25B PRO* 1.3 76.5 - - - +
27B ARG* 1.3 61.9 + - - +
29B LEU* 3.3 12.2 + - - +
30B GLY 3.6 0.3 + - - -
31B ALA* 3.3 20.1 + - - +
33B VAL* 3.7 23.3 - - + -
80B LEU* 5.3 4.0 - - + -
228B GLY* 3.4 47.6 - - - +
229B LEU* 4.0 9.0 - - + -
231B LEU* 5.2 2.9 - - + -
232B VAL* 3.7 7.6 - - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 5.4 2.2 + - - -
16A HIS* 4.1 22.0 + - - -
20A SER* 4.7 12.7 + - - +
23A GLU* 3.0 27.1 + - - -
24A PHE* 3.4 32.1 - - + +
269A VAL* 3.7 21.1 - - + +
272A GLN* 2.9 13.5 + - - -
23B GLU* 3.0 36.0 + - - +
24B PHE 2.9 4.3 + - - +
26B MET* 1.3 73.5 - - - +
28B ARG* 1.3 57.9 + - - +
29B LEU 3.0 2.0 - - - -
30B GLY* 2.7 22.0 + - - -
31B ALA 3.4 18.8 - - - +
32B ASN* 5.7 0.2 - - - +
33B VAL* 2.7 38.8 + - + +
35B PRO* 3.8 13.7 - - - +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.9 2.4 - - + -
28A ARG* 3.4 29.5 - - - +
272A GLN* 3.0 30.5 + - - +
273A ASP* 3.8 7.5 + - - -
24B PHE* 2.8 39.1 + - + +
25B PRO* 3.3 12.3 + - + +
27B ARG* 1.3 76.2 - - - +
29B LEU* 1.3 65.3 + - + +
30B GLY 3.1 1.1 + - - -
272B GLN* 3.2 41.1 + - + +
273B ASP* 2.9 32.5 + - - +
275B ILE* 4.7 10.5 - - + -
276B ALA* 3.9 22.4 - - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 3.2 13.8 + - - +
26B MET* 3.7 9.9 - - - +
27B ARG 3.0 1.4 - - - -
28B ARG* 1.3 79.6 - - - +
30B GLY* 1.3 56.0 + - - +
31B ALA 3.5 1.1 - - - -
229B LEU* 4.1 24.2 - - + -
232B VAL* 4.1 18.2 - - + -
233B LYS* 4.5 17.0 - - + -
236B GLN* 3.2 22.1 + - - +
246B HIS* 4.1 23.3 - - + +
247B VAL* 6.2 0.2 - - + -
275B ILE* 3.7 14.6 - - + +
276B ALA* 3.7 31.4 - - + +
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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