Contacts of the helix formed by residues 30 - 39 (chain A) in PDB entry 1TLH
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 ARG 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL 5.3 0.2 - - - -
28A GLU 3.0 9.7 + - - +
29A ASN* 1.4 68.8 - - - +
31A ALA* 1.3 62.2 + - - +
33A PHE* 3.8 5.8 + - - +
34A ILE* 3.5 28.8 + - + +
51A GLN* 5.0 15.7 - - - +
86A MET 5.2 1.4 + - - -
87A TYR* 2.7 57.4 + - + +
88A THR* 4.4 16.1 - - + +
89A ASN* 4.7 5.1 - - - +
604B SER* 5.7 5.7 + - - -
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Residues in contact with ALA 31 (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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29A ASN* 3.3 1.7 - - + -
30A ARG* 1.3 78.6 - - - +
32A ASN* 1.4 57.7 + - - +
34A ILE* 3.3 4.5 + - - +
35A ALA* 2.9 32.2 + - - +
51A GLN* 5.7 4.7 - - - +
598B LEU* 3.6 23.7 - - + +
602B SER* 3.3 34.5 - - - +
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Residues in contact with ASN 32 (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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26A ILE* 3.8 26.9 + - - +
29A ASN* 2.9 38.0 + - + +
31A ALA* 1.4 76.4 - - - +
33A PHE* 1.4 62.9 + - - +
35A ALA* 3.4 7.1 + - - +
36A PHE* 3.0 41.6 + - - -
591B GLU* 4.0 12.4 + - - +
594B ALA* 5.0 2.1 - - - +
595B LEU* 3.8 33.7 - - + +
598B LEU* 4.8 0.8 - - - +
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Residues in contact with PHE 33 (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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11A ILE* 6.4 0.2 - - + -
15A ALA* 4.1 21.5 - - + -
18A LEU* 3.7 29.2 - - + -
19A ILE* 5.4 3.1 - - + -
26A ILE 3.8 5.4 + - - +
27A VAL* 3.6 49.4 - - + +
29A ASN 3.1 9.6 + - - +
30A ARG* 3.9 6.1 - - - +
32A ASN* 1.4 75.5 - - - +
34A ILE* 1.4 65.1 + - + +
36A PHE* 3.2 21.3 + - - +
37A LEU* 3.6 13.3 - - + +
54A PHE* 3.8 33.0 - + - -
80A VAL* 4.5 17.0 - - + -
83A TYR* 6.0 3.6 - - + -
84A LEU* 5.6 7.9 - - + -
88A THR* 5.2 8.3 - - + -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG* 3.5 17.0 + - + +
31A ALA* 3.3 4.6 + - - +
33A PHE* 1.4 81.4 - - + +
35A ALA* 1.4 57.8 + - - +
37A LEU* 3.1 7.9 + - - +
38A ASN* 3.0 29.3 + - - +
49A LEU* 3.2 28.5 - - + +
50A ASN* 5.0 2.0 - - - -
51A GLN* 3.5 31.9 - - + +
54A PHE* 3.6 48.9 - - + -
55A ARG* 6.1 0.4 - - + -
88A THR* 4.9 11.7 - - + -
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Residues in contact with ALA 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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31A ALA 2.9 20.8 + - - +
32A ASN* 3.5 9.0 - - - +
34A ILE* 1.4 76.3 - - - +
36A PHE* 1.3 55.5 + - - +
38A ASN* 3.8 8.3 - - - +
39A GLU* 2.9 28.4 + - - +
594B ALA* 3.9 24.4 - - + +
595B LEU* 5.7 0.9 - - + -
597B LYS* 6.0 2.1 - - + +
598B LEU* 5.0 13.2 - - + +
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Residues in contact with PHE 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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14A VAL* 5.5 1.8 - - - +
18A LEU* 3.9 26.5 - - + -
26A ILE* 3.6 22.4 - - + -
32A ASN* 3.0 41.4 + - - -
33A PHE* 3.2 13.0 + - - +
35A ALA* 1.3 73.0 - - - +
37A LEU* 1.3 64.2 + - + +
39A GLU* 3.5 18.0 - - - +
40A ILE* 3.8 11.1 - - - +
563B PHE* 5.7 4.5 - + - -
587B ILE* 3.3 43.1 - - + -
590B ILE* 3.3 31.0 - - + +
591B GLU* 3.4 21.8 - - + -
594B ALA* 4.7 4.0 - - + -
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Residues in contact with LEU 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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11A ILE* 4.0 29.2 - - + +
14A VAL* 4.0 25.4 - - + -
15A ALA* 5.0 8.7 - - + -
18A LEU* 4.4 17.9 - - + -
33A PHE* 3.6 18.4 - - + +
34A ILE 3.1 9.7 + - - +
36A PHE* 1.3 80.8 - - - +
38A ASN* 1.3 62.0 + - - +
40A ILE* 3.2 20.4 - - + +
41A GLY 3.6 2.4 + - - -
42A VAL* 3.6 27.7 - - + +
49A LEU* 4.0 15.5 - - + -
54A PHE* 4.2 20.2 - - + -
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Residues in contact with ASN 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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34A ILE* 3.0 25.0 + - - +
35A ALA* 4.1 7.5 - - - +
36A PHE 3.5 0.2 - - - -
37A LEU* 1.3 74.4 - - - +
39A GLU* 1.4 56.9 + - - +
41A GLY* 2.8 26.0 + - - +
42A VAL 4.6 3.9 + - - +
48A LYS* 3.6 21.0 - - + +
49A LEU* 3.1 53.5 + - - +
50A ASN* 4.5 4.2 - - - +
597B LYS* 4.9 8.3 + - + -
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Residues in contact with GLU 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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35A ALA 2.9 12.8 + - - +
36A PHE* 3.5 16.4 - - - +
38A ASN* 1.4 73.9 - - - +
40A ILE* 1.4 63.7 + - + +
41A GLY 3.7 0.3 + - - -
590B ILE* 4.3 20.4 - - + +
593B LYS* 4.4 21.4 - - - +
594B ALA* 3.7 28.0 - - + +
597B LYS* 4.1 29.4 + - + +
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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