Contacts of the helix formed by residues 34 - 45 (chain A) in PDB entry 4TLG
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 ASP 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.5 3.1 - - - +
32A ASN* 2.9 21.9 + - - +
33A ALA* 1.3 82.2 - - - +
35A ASP* 1.3 64.2 + - - +
36A TYR* 3.5 13.2 - - + +
37A PHE* 2.9 30.0 + - - +
38A LEU* 3.3 12.1 + - - +
145A LYS* 3.1 19.6 + - - -
508A EDO 2.7 33.8 + - - +
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Residues in contact with ASP 35 (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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5A VAL* 4.0 18.1 - - + +
16A LEU* 3.7 29.4 - - + +
20A ARG* 2.9 27.0 + - - +
34A ASP* 1.3 72.0 - - - +
36A TYR* 1.3 67.5 + - + +
38A LEU* 3.4 4.3 + - - +
39A LEU* 2.9 29.8 + - + +
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Residues in contact with TYR 36 (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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4A ARG* 5.8 1.1 - - - -
5A VAL* 3.8 42.3 - - + +
34A ASP* 3.2 23.0 - - + +
35A ASP* 1.3 81.0 - - + +
37A PHE* 1.3 63.6 + - - +
39A LEU* 3.5 4.0 + - - +
40A ARG* 3.5 23.1 + - - +
43A ARG* 4.8 2.1 + - - -
145A LYS* 3.7 42.6 - - + +
147A GLU* 3.6 34.5 - - + -
508A EDO 4.2 7.6 - - - -
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Residues in contact with PHE 37 (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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30A LEU* 4.0 14.1 - - + -
31A PRO* 3.8 27.4 - - + -
32A ASN* 3.0 38.8 - - + +
34A ASP* 2.9 17.4 + - - +
36A TYR* 1.3 76.7 - - - +
38A LEU* 1.3 74.3 + - + +
40A ARG* 3.2 31.1 + - - +
41A TRP* 3.1 45.3 + + - -
56A LEU* 3.7 23.8 - - + -
59A HIS* 5.1 0.9 - + - -
502A EDO 3.3 22.9 - - - -
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Residues in contact with LEU 38 (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* 3.8 24.5 - - + -
19A PHE* 3.6 19.4 - - + -
20A ARG* 3.5 52.7 - - + +
23A LEU* 3.8 24.9 - - + -
27A LEU* 5.0 2.7 - - + -
30A LEU* 4.2 13.7 - - + -
33A ALA 4.6 2.0 - - - +
34A ASP 3.3 11.0 + - - +
35A ASP 3.9 3.4 - - - +
37A PHE* 1.3 93.8 - - + +
39A LEU* 1.3 61.9 + - - +
41A TRP* 3.2 14.5 + - - +
42A LEU* 3.2 10.9 + - - +
56A LEU* 4.5 2.2 - - + -
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Residues in contact with LEU 39 (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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3A SER 4.1 7.2 - - - +
4A ARG 4.2 2.7 - - - -
5A VAL* 3.4 42.4 - - + +
12A GLN 5.7 0.2 - - - +
16A LEU* 4.4 20.0 - - + -
35A ASP* 2.9 26.4 + - + +
36A TYR* 3.9 4.7 - - - +
37A PHE 3.2 0.2 - - - -
38A LEU* 1.3 75.0 - - - +
40A ARG* 1.3 59.4 + - - +
42A LEU* 4.2 10.5 - - + -
43A ARG* 2.9 48.7 + - - +
47A PHE* 3.9 32.8 - - + -
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Residues in contact with ARG 40 (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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36A TYR 3.5 14.0 + - - +
37A PHE* 3.2 32.2 + - - +
39A LEU* 1.3 76.6 - - - +
41A TRP* 1.3 66.0 + - + +
43A ARG* 3.9 20.2 - - - +
44A ALA* 3.1 24.5 + - - +
132A LEU* 5.0 4.4 - - - +
147A GLU* 5.3 9.6 + - - +
183A PRO* 2.9 51.9 + - + +
184A GLU* 3.5 24.4 - - + +
185A THR* 3.4 15.8 - - - +
502A EDO 2.7 43.4 + - - -
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Residues in contact with TRP 41 (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 PHE* 4.1 8.1 - - + -
37A PHE* 3.1 56.3 + + - -
38A LEU* 3.2 9.3 + - - +
40A ARG* 1.3 76.9 - - - +
42A LEU* 1.3 66.1 + - - +
44A ALA* 3.4 6.1 + - - +
45A ARG* 3.3 18.7 + - - +
52A SER* 3.4 24.8 + - - +
55A MET* 3.7 29.0 - - + +
56A LEU* 3.6 27.8 - - + -
59A HIS* 3.6 26.0 - + + -
180A ALA 3.5 19.3 - - - -
181A ASN 3.4 20.4 - - - -
183A PRO* 3.6 18.6 - - + -
502A EDO 3.7 17.9 - - - -
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Residues in contact with LEU 42 (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* 4.9 0.9 - - + +
16A LEU* 3.9 33.9 - - + -
19A PHE* 3.6 37.0 - - + -
38A LEU 3.2 7.1 + - - +
39A LEU* 3.8 10.5 - - + +
41A TRP* 1.3 77.4 - - - +
43A ARG* 1.3 61.9 + - - +
45A ARG 3.1 3.1 + - - -
46A ASN 3.0 4.3 + - - -
47A PHE* 2.8 68.8 + - + -
49A LEU* 4.4 9.9 - - + -
52A SER* 3.5 21.1 - - - +
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Residues in contact with ARG 43 (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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3A SER* 3.0 42.7 + - - +
4A ARG* 3.4 42.8 - - - +
5A VAL 4.8 0.2 - - - +
36A TYR 4.8 1.8 + - - -
39A LEU* 2.9 36.6 + - + +
40A ARG* 3.9 23.5 - - - +
42A LEU* 1.3 75.5 - - - +
44A ALA* 1.3 61.2 + - - +
45A ARG 3.2 1.2 + - - -
46A ASN* 3.3 11.1 + - - +
47A PHE* 4.1 14.6 - - + -
147A GLU* 4.9 2.4 + - - -
184A GLU* 2.8 39.0 + - - +
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Residues in contact with ALA 44 (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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40A ARG 3.1 18.0 + - - +
41A TRP 3.7 6.1 - - - +
42A LEU 3.2 0.4 - - - -
43A ARG* 1.3 76.4 - - - +
45A ARG* 1.3 79.6 + - - +
46A ASN 3.7 0.2 - - - -
55A MET* 3.8 28.5 - - + -
183A PRO* 4.2 9.6 - - + -
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Residues in contact with ARG 45 (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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41A TRP 3.3 3.2 + - - +
42A LEU 3.1 3.0 + - - -
43A ARG 3.1 0.6 - - - -
44A ALA* 1.3 95.5 + - - +
46A ASN* 1.3 68.6 + - - +
47A PHE 3.2 2.7 - - - -
48A ASP* 2.9 19.6 + - - +
51A LYS* 3.9 39.5 + - + +
52A SER* 3.5 20.9 - - - +
55A MET* 3.6 48.9 - - - +
180A ALA* 5.7 2.6 - - - +
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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