Contacts of the helix formed by residues 25 - 35 (chain B) in PDB entry 1TDR
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 PRO 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.2 9.6 - - - +
24B LEU* 1.3 87.6 - - - +
26B ALA* 1.3 55.4 + - - +
28B LEU* 3.2 14.2 + - + +
29B ALA* 3.0 27.9 + - - +
146B GLN* 3.0 48.9 - - + +
147B ASN* 3.2 10.3 - - - +
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Residues in contact with ALA 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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24B LEU* 3.0 0.4 - - + -
25B PRO* 1.3 74.6 - - - +
27B ASP* 1.3 65.3 + - - +
29B ALA* 3.4 7.2 + - - +
30B TRP* 3.0 25.1 + - - +
147B ASN* 3.3 17.2 + - - +
151B TYR* 3.2 35.0 - - + +
153B PHE* 3.8 7.0 - - + -
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Residues in contact with ASP 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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7B ALA* 4.0 8.0 - - - +
22B TRP* 5.6 2.9 + - - +
24B LEU* 2.8 33.8 + - + +
26B ALA* 1.3 78.1 - - - +
28B LEU* 1.3 59.2 + - - +
30B TRP* 3.5 2.3 + - - +
31B PHE* 3.0 24.1 + - - +
113B THR* 2.8 29.2 + - + -
151B TYR* 5.0 1.3 - - + -
153B PHE* 4.4 6.7 - - + -
170B MTX 2.5 50.7 + - - -
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Residues in contact with LEU 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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24B LEU 3.1 15.4 + - - +
25B PRO* 3.6 14.4 - - + +
26B ALA 3.2 0.2 - - - -
27B ASP* 1.3 75.8 - - - +
29B ALA* 1.3 54.9 + - - +
31B PHE* 3.2 6.8 - - + +
32B LYS* 2.7 35.7 + - - +
170B MTX 3.6 90.5 - - + +
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Residues in contact with ALA 29 (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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25B PRO 3.0 15.9 + - - +
26B ALA* 3.9 7.9 - - - +
27B ASP 3.4 0.2 - - - -
28B LEU* 1.3 74.7 - - - +
30B TRP* 1.3 56.1 + - - +
32B LYS* 3.5 6.3 + - - +
33B ARG* 2.9 30.0 + - - +
170B MTX 5.0 2.6 - - - +
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Residues in contact with TRP 30 (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* 4.3 11.2 - - + +
26B ALA 3.0 17.9 + - - +
27B ASP* 3.8 7.0 - - - +
29B ALA* 1.3 72.2 - - - +
31B PHE* 1.3 74.7 + - - +
33B ARG* 4.0 18.4 - - - +
34B ASN* 3.1 52.7 + - - +
111B TYR* 4.2 20.4 - + + +
112B LEU 4.6 2.2 + - - -
113B THR* 3.7 23.5 + - - -
137B PHE* 4.0 18.8 - + - -
153B PHE* 3.7 52.0 - + + -
154B LYS 4.4 7.0 - - - -
155B ILE* 4.1 24.5 - - + -
170B MTX 4.3 4.6 + - - -
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Residues in contact with PHE 31 (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* 3.8 16.6 - - + +
27B ASP 3.0 15.6 + - - +
28B LEU* 3.2 13.7 - - + +
30B TRP* 1.3 82.0 - - - +
32B LYS* 1.3 65.7 + - - +
34B ASN* 3.0 8.8 + - - +
35B THR* 3.0 30.3 + - + +
54B LEU* 4.0 5.8 - - + -
57B ARG* 3.6 19.7 - - - -
94B ILE* 3.6 36.6 - - + -
170B MTX 3.5 87.7 - + + +
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Residues in contact with LYS 32 (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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28B LEU 2.7 19.5 + - - +
29B ALA* 3.9 6.3 - - - +
31B PHE* 1.3 70.6 - - - +
33B ARG* 1.3 68.5 + - - +
34B ASN 2.8 1.4 + - - -
35B THR* 3.0 6.9 + - - -
36B LEU* 3.0 48.6 + - + +
55B PRO* 6.5 1.6 - - - -
57B ARG* 4.0 12.1 - - - +
170B MTX 3.3 45.1 + - + +
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Residues in contact with ARG 33 (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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29B ALA 2.9 21.1 + - - +
30B TRP* 4.2 17.6 - - - +
32B LYS* 1.3 74.9 - - - +
34B ASN* 1.3 77.5 + - - +
36B LEU* 4.4 10.3 + - - +
38B LYS* 5.3 1.2 + - - -
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Residues in contact with ASN 34 (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* 4.3 7.2 - - + -
30B TRP* 3.1 60.9 + - - +
31B PHE 3.0 4.8 + - - +
32B LYS 3.0 1.8 - - - -
33B ARG* 1.3 89.3 - - - +
35B THR* 1.3 59.3 + - - +
36B LEU 3.7 0.4 - - - -
38B LYS* 2.8 29.9 + - - +
92B MET* 3.3 12.4 - - + +
111B TYR* 3.2 31.9 - - + -
155B ILE* 5.0 2.1 - - - +
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Residues in contact with THR 35 (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* 4.3 6.7 - - + -
31B PHE* 3.0 39.1 + - + +
32B LYS* 3.8 0.5 - - - -
34B ASN* 1.3 77.6 - - - +
36B LEU* 1.3 67.2 + - - +
38B LYS* 3.1 15.5 - - - +
40B VAL* 3.7 26.9 - - + +
57B ARG* 2.5 47.1 + - - +
92B MET* 4.0 15.5 - - + -
94B ILE* 3.9 7.9 - - + -
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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