Contacts of the helix formed by residues 19 - 31 (chain A) in PDB entry 3TQI
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 TYR 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A SER* 2.9 15.4 + - - +
18A GLN* 1.3 106.1 + - + +
20A ALA* 1.3 65.1 + - - +
21A GLN 3.3 6.7 - - - +
22A LEU* 3.4 24.1 - - + +
23A ILE* 3.1 22.9 + - - +
57A SER* 5.8 0.2 - - - -
108A PHE* 6.4 1.6 - + - -
140A TRP* 5.2 10.8 + - - -
181A HIS* 4.5 18.6 - + - -
183A GLU* 3.0 19.4 - - - +
184A VAL* 3.8 25.4 - - + +
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Residues in contact with ALA 20 (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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12A ILE* 5.6 0.2 - - - -
14A ASP* 3.6 34.8 - - - +
16A GLY 3.9 0.9 - - - +
17A SER* 3.1 13.7 + - - +
18A GLN 3.3 0.8 - - - -
19A TYR* 1.3 71.0 - - - +
21A GLN* 1.3 60.8 + - + +
23A ILE* 2.9 35.0 + - - +
24A ALA* 3.4 5.0 + - - +
36A LEU* 4.0 17.5 - - + +
57A SER* 4.2 14.4 - - - +
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Residues in contact with GLN 21 (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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18A GLN 3.6 10.7 + - - +
19A TYR 3.3 6.1 - - - -
20A ALA* 1.3 75.2 - - - +
22A LEU* 1.3 68.9 + - - +
24A ALA* 4.6 6.1 - - - -
25A ARG* 4.9 4.8 + - + +
36A LEU* 3.6 11.0 - - + +
338A PRO* 3.7 27.3 + - - +
341A ILE* 3.0 42.2 - - + +
379A PHE* 3.8 15.1 - - + -
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Residues in contact with LEU 22 (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 TYR* 3.4 40.6 - - + +
20A ALA 3.1 0.2 + - - -
21A GLN* 1.3 81.5 - - - +
23A ILE* 1.3 61.6 + - - +
24A ALA 3.3 4.0 - - - +
25A ARG* 3.5 46.7 - - + +
26A ARG* 3.0 61.5 + - - +
183A GLU* 3.9 17.0 - - + +
184A VAL* 4.4 7.4 - - + -
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Residues in contact with ILE 23 (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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12A ILE* 4.2 13.0 - - + -
19A TYR 3.1 17.0 - - - +
20A ALA* 2.9 12.3 + - - +
22A LEU* 1.3 75.7 - - - +
24A ALA* 1.3 65.8 + - - +
26A ARG* 3.2 4.2 + - - +
27A VAL* 3.1 25.2 + - - +
55A ILE* 3.9 34.8 - - + -
57A SER* 3.6 28.0 - - - -
85A ILE* 3.4 30.3 - - + -
181A HIS* 5.9 0.2 - - + -
183A GLU* 3.5 19.7 - - + +
194A LEU* 4.6 8.0 - - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.3 25.9 - - + +
20A ALA 3.4 8.9 + - - +
21A GLN* 4.6 1.6 - - - -
22A LEU 4.4 1.6 - - - +
23A ILE* 1.3 79.4 - - - +
25A ARG* 1.3 58.2 + - - +
27A VAL* 3.1 5.2 + - - +
28A ARG* 2.9 32.2 + - - +
34A CYS* 3.5 7.1 - - - -
36A LEU* 4.8 11.0 - - + +
337A TYR* 5.8 0.4 - - + -
379A PHE* 3.7 27.1 - - + -
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Residues in contact with ARG 25 (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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21A GLN* 4.9 3.6 + - - +
22A LEU* 3.5 47.3 + - + +
23A ILE 3.2 0.6 - - - -
24A ALA* 1.3 76.8 - - - +
26A ARG* 1.3 62.1 + - - +
28A ARG* 3.2 10.4 + - - +
29A GLU* 2.9 29.8 + - - +
379A PHE* 3.7 36.1 - - + -
380A LYS* 6.1 0.4 - - - +
381A ASP* 3.1 42.6 + - - +
384A ARG* 6.1 0.8 - - - +
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Residues in contact with ARG 26 (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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22A LEU* 3.0 45.6 + - - +
23A ILE 3.2 4.5 + - - +
25A ARG* 1.3 78.9 - - - +
27A VAL* 1.3 60.9 + - - +
29A GLU* 3.2 26.3 + - - +
30A ILE* 3.1 31.0 + - + +
182A PRO 5.1 0.8 + - - -
183A GLU* 3.0 36.3 + - - +
184A VAL* 4.7 0.8 - - - +
185A THR* 3.8 26.1 - - - +
191A HIS* 4.6 23.3 - - + +
194A LEU* 4.1 15.9 - - + -
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Residues in contact with VAL 27 (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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10A ILE* 4.2 18.8 - - + -
12A ILE* 4.4 6.1 - - + -
23A ILE* 3.1 17.7 + - + +
24A ALA 3.1 7.5 + - - +
26A ARG* 1.3 74.4 - - + +
28A ARG* 1.3 63.2 + - - +
30A ILE* 3.3 19.2 + - + +
31A GLY 3.4 0.7 + - - -
32A VAL* 3.2 31.0 + - + +
34A CYS* 4.0 17.9 - - + -
55A ILE* 4.3 23.1 - - + -
194A LEU* 5.0 6.1 - - + -
198A VAL* 4.3 13.9 - - + -
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Residues in contact with ARG 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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24A ALA 2.9 21.6 + - - +
25A ARG* 3.2 7.4 + - - +
27A VAL* 1.3 76.2 - - - +
29A GLU* 1.3 62.4 + - - +
31A GLY* 3.1 14.0 + - - -
32A VAL 3.6 15.9 - - - -
33A TYR* 3.7 17.3 + - - +
34A CYS* 2.8 38.0 + - - +
208A TRP* 3.7 31.0 - - + +
337A TYR* 3.9 17.4 - - - -
377A GLU* 2.7 30.3 + - - +
379A PHE* 4.0 14.3 - - + -
382A GLU* 3.0 41.8 + - + +
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Residues in contact with GLU 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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25A ARG 2.9 11.3 + - - +
26A ARG* 3.4 38.4 + - - +
28A ARG* 1.3 74.5 - - - +
30A ILE* 1.3 65.4 + - + +
31A GLY* 3.3 1.4 + - - -
381A ASP* 5.9 2.5 - - - -
385A LYS* 4.7 18.8 - - - +
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Residues in contact with ILE 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 ARG* 3.1 19.4 + - + +
27A VAL* 3.5 16.2 - - - +
28A ARG 3.3 0.2 - - - -
29A GLU* 1.3 77.3 - - + +
31A GLY* 1.3 56.9 + - - +
32A VAL* 4.5 6.1 - - + -
191A HIS* 4.3 6.1 - - + +
194A LEU* 4.0 13.7 - - + +
195A ALA* 3.6 37.5 - - + +
198A VAL* 4.6 9.4 - - + -
199A ILE* 3.7 33.8 - - + +
206A PRO* 3.6 13.7 - - - +
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Residues in contact with GLY 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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27A VAL 3.4 0.2 + - - -
28A ARG 3.1 9.9 + - - -
29A GLU 3.1 4.9 - - - -
30A ILE* 1.3 78.3 - - - +
32A VAL* 1.3 62.1 + - - +
206A PRO* 3.2 7.6 - - - +
207A ASN 3.0 13.0 + - - -
208A TRP* 2.8 42.4 + - - -
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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