Contacts of the helix formed by residues 27 - 37 (chain A) in PDB entry 1TTV
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 THR 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PRO* 1.3 73.6 - - - +
28A PRO* 1.3 62.6 - - - +
29A LEU* 2.7 10.0 + - - -
30A LEU* 2.9 15.4 + - - +
31A LEU* 2.6 33.3 + - - +
81A LEU* 3.4 18.0 - - + +
101A ARG 4.7 2.2 - - - +
102A ASN* 2.6 46.5 + - - +
103A LEU 4.0 1.1 - - - +
104A VAL* 4.0 18.4 - - + +
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Residues in contact with PRO 28 (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 PRO 3.6 2.0 - - - +
27A THR* 1.3 86.0 - - - +
29A LEU* 1.3 61.2 + - - +
31A LEU* 3.5 16.4 - - + +
32A SER* 3.5 18.2 + - - -
104A VAL* 3.9 17.9 - - + -
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Residues in contact with LEU 29 (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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27A THR* 2.7 7.0 + - - +
28A PRO* 1.3 73.3 - - - +
30A LEU* 1.3 65.0 + - - +
31A LEU 3.1 2.0 + - - -
32A SER* 3.3 13.2 + - - -
33A LEU* 3.2 15.9 - - + +
77A PRO* 3.6 30.3 - - + +
80A GLU* 2.8 41.7 - - + +
81A LEU* 3.3 39.9 - - + -
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Residues in contact with LEU 30 (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 PRO* 4.0 18.8 - - + -
27A THR* 2.9 19.3 + - - +
29A LEU* 1.3 77.4 - - - +
31A LEU* 1.3 64.4 + - - +
33A LEU* 2.9 45.7 + - + +
34A LEU* 3.1 14.4 + - + +
49A VAL* 4.1 17.0 - - + -
53A LEU* 3.5 25.4 - - + -
78A LEU* 4.7 0.2 - - + -
81A LEU* 3.5 15.5 - - + +
82A PHE* 5.1 0.9 - - + -
99A ILE* 4.4 11.4 - - + +
102A ASN* 3.8 24.5 - - + +
103A LEU* 5.0 0.9 - - + -
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Residues in contact with LEU 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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25A GLN* 4.9 5.8 - - + +
26A PRO* 3.5 28.2 - - + +
27A THR 2.6 15.4 + - - +
28A PRO* 3.5 16.6 - - + +
30A LEU* 1.3 70.6 - - - +
32A SER* 1.3 51.9 + - - +
34A LEU* 2.7 28.2 + - - +
35A LYS* 2.7 32.4 + - + +
42A GLU* 3.1 43.5 - - + +
44A PHE* 3.6 20.0 - - + -
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Residues in contact with SER 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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28A PRO 3.5 8.1 + - - -
29A LEU* 3.3 12.6 + - - -
31A LEU* 1.3 78.7 - - - +
33A LEU* 1.3 61.1 + - - +
35A LYS* 2.9 15.0 + - - +
36A SER* 2.8 33.3 + - - -
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Residues in contact with LEU 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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29A LEU* 3.2 14.1 - - + +
30A LEU* 3.1 41.5 - - + +
32A SER* 1.3 78.3 - - - +
34A LEU* 1.3 57.3 + - + +
36A SER* 3.6 0.4 + - - -
37A ALA* 2.9 29.8 + - - +
53A LEU* 4.8 1.6 - - + -
56A TYR* 3.3 39.4 - - + +
77A PRO* 3.4 32.1 - - + +
78A LEU* 3.8 35.0 - - + -
81A LEU* 4.2 4.3 - - + -
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Residues in contact with LEU 34 (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 PRO* 3.4 37.0 - - + -
30A LEU* 3.4 15.3 - - + +
31A LEU* 2.7 12.3 + - - +
33A LEU* 1.3 71.0 - - - +
35A LYS* 1.3 59.5 + - - +
37A ALA* 2.9 12.0 + - - -
38A GLY 3.1 0.3 + - - -
39A ALA* 2.6 46.4 + - + +
44A PHE* 3.6 22.0 - - + -
49A VAL* 3.7 29.4 - - + +
52A HIS* 3.6 20.4 - - + -
53A LEU* 3.8 13.0 - - + +
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Residues in contact with LYS 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 LEU* 2.7 40.2 + - + +
32A SER* 2.9 19.0 + - - +
34A LEU* 1.3 74.5 - - - +
36A SER* 1.3 58.2 + - - +
38A GLY* 3.7 5.2 + - - -
39A ALA* 3.1 20.5 - - + +
40A GLN* 3.0 29.4 + - - +
41A LYS 3.2 15.5 - - - +
42A GLU* 4.5 3.9 - - - +
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Residues in contact with SER 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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32A SER* 2.8 17.8 + - - -
33A LEU* 4.1 4.3 - - - -
35A LYS* 1.3 70.0 - - - +
37A ALA* 1.3 57.1 + - - +
38A GLY 3.1 8.8 + - - -
56A TYR* 5.2 2.2 - - - -
60A LYS* 4.7 18.0 + - - -
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Residues in contact with ALA 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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33A LEU 2.9 18.1 + - - +
34A LEU 2.9 6.8 + - - +
36A SER* 1.3 77.2 - - - +
38A GLY* 1.3 56.5 + - - +
39A ALA 3.5 0.7 - - - -
52A HIS* 2.9 40.4 + - + +
55A GLN* 3.5 25.6 + - + +
56A TYR* 4.0 10.5 - - + +
60A LYS* 4.8 4.9 - - - +
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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