Contacts of the helix formed by residues 19 - 31 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER* 2.7 19.1 + - - +
18C GLN* 1.3 101.7 + - + +
20C ALA* 1.3 66.1 + - - +
21C GLN 2.9 11.7 - - - +
22C LEU* 3.5 21.2 - - + +
23C ILE* 3.3 17.2 + - - +
57C SER* 5.8 0.2 - - - -
108C PHE* 6.0 4.0 - + - -
140C TRP* 4.5 16.0 + - - -
181C HIS* 4.3 22.7 - + + -
183C GLU* 3.0 24.0 - - - +
184C VAL* 4.8 20.9 - - + +
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASP* 3.5 37.5 - - - +
16C GLY 3.7 1.3 - - - +
17C SER* 2.9 15.1 + - - +
18C GLN 3.3 0.6 - - - -
19C TYR* 1.3 79.0 - - - +
21C GLN* 1.3 61.2 + - + +
23C ILE* 3.0 21.7 + - - +
24C ALA 3.5 3.1 + - - -
36C LEU* 3.9 16.9 - - + +
57C SER* 4.2 19.1 - - - +
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN 3.8 6.8 + - - +
19C TYR* 2.9 12.8 - - - +
20C ALA* 1.3 75.7 - - + +
22C LEU* 1.3 68.1 + - - +
24C ALA* 4.4 6.5 - - - -
25C ARG* 4.7 6.4 + - - +
36C LEU* 3.7 21.6 - - + +
338C PRO* 4.0 18.7 + - - +
341C ILE* 3.6 32.0 - - + +
379C PHE* 3.8 20.0 - - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.5 28.3 - - + +
21C GLN* 1.3 82.3 - - - +
23C ILE* 1.3 61.2 + - - +
24C ALA 3.6 4.2 - - - +
25C ARG* 3.6 49.5 - - + +
26C ARG* 2.9 49.8 + - - +
183C GLU* 3.8 35.2 - - + +
184C VAL* 4.4 4.9 - - + +
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.7 15.0 - - + -
19C TYR 3.3 4.9 + - - +
20C ALA 3.0 14.7 + - - +
22C LEU* 1.3 75.9 - - - +
24C ALA* 1.3 64.1 + - - +
26C ARG* 3.2 5.8 + - - +
27C VAL* 3.0 28.5 + - + +
55C ILE* 3.7 35.2 - - + -
57C SER* 3.3 35.9 - - - -
85C ILE* 3.7 20.0 - - + -
183C GLU* 3.2 28.4 - - + +
194C LEU* 4.7 8.7 - - + +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.4 21.5 - - + +
20C ALA 3.5 5.6 + - - +
21C GLN* 4.4 2.9 - - - -
22C LEU 4.3 4.9 - - - +
23C ILE* 1.3 81.4 - - - +
25C ARG* 1.3 61.6 + - - +
27C VAL 3.3 1.9 + - - -
28C ARG* 3.0 27.6 + - - +
34C CYS* 3.3 9.8 - - - -
36C LEU* 4.9 14.4 - - + +
337C TYR* 5.5 0.7 - - + -
379C PHE* 3.6 27.1 - - + -
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN* 4.7 5.6 + - - +
22C LEU* 3.6 43.5 - - + +
23C ILE 3.2 0.8 - - - -
24C ALA* 1.3 74.5 - - - +
26C ARG* 1.3 64.9 + - + +
28C ARG* 3.2 9.5 + - - +
29C GLU* 2.9 30.1 + - - +
379C PHE* 3.6 41.3 - - + -
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 2.9 43.1 + - - +
23C ILE 3.2 3.8 + - - +
25C ARG* 1.3 81.5 - - - +
27C VAL* 1.3 62.2 + - - +
29C GLU* 3.2 26.2 + - - +
30C ILE* 3.0 30.9 + - + +
182C PRO 4.9 1.2 + - - -
183C GLU* 2.9 28.2 + - - +
184C VAL* 4.4 0.8 - - - +
185C THR* 3.7 28.3 - - - +
191C HIS* 4.4 23.1 - - + +
194C LEU* 3.8 26.9 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.1 17.7 - - + -
12C ILE* 4.2 5.4 - - + -
23C ILE* 3.0 21.4 + - + +
24C ALA 3.5 7.2 - - - +
26C ARG* 1.3 77.4 - - + +
28C ARG* 1.3 62.5 + - - +
30C ILE* 3.2 19.7 + - + +
31C GLY 3.2 8.7 + - - -
32C VAL* 3.3 26.0 + - + +
34C CYS* 3.9 18.4 - - + -
55C ILE* 4.1 26.2 - - + -
194C LEU* 5.4 4.5 - - + -
198C VAL* 4.3 13.7 - - + -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 3.0 19.4 + - - +
25C ARG* 3.5 7.9 - - - +
27C VAL* 1.3 75.4 - - - +
29C GLU* 1.3 58.7 + - - +
31C GLY* 3.0 19.6 + - - -
32C VAL 3.7 9.6 - - - -
33C TYR* 3.6 17.2 + - - -
34C CYS* 3.0 41.7 + - - +
208C TRP* 3.6 44.0 - - + +
337C TYR* 3.9 15.6 - - - -
377C GLU* 2.8 31.9 + - - +
378C LEU* 4.1 5.3 - - - +
379C PHE* 3.8 26.1 - - + +
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG 2.9 15.5 + - - +
26C ARG* 3.2 33.1 + - - +
28C ARG* 1.3 76.7 - - - +
30C ILE* 1.3 63.3 + - + +
31C GLY* 3.2 1.6 + - - -
191C HIS* 6.1 0.2 - - - +
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.0 23.3 + - + +
27C VAL* 3.2 12.5 + - - +
29C GLU* 1.3 75.6 - - + +
31C GLY* 1.3 55.3 + - - +
32C VAL* 4.8 1.1 - - + -
191C HIS* 4.2 6.7 - - + +
194C LEU* 3.8 16.2 - - + +
195C ALA* 3.4 41.1 - - + +
198C VAL* 4.4 13.2 - - + -
199C ILE* 3.8 29.8 - - + +
206C PRO* 3.4 14.9 - - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL 3.2 0.4 + - - -
28C ARG 3.0 13.7 + - - -
29C GLU 3.1 1.7 - - - -
30C ILE* 1.3 79.6 - - - +
32C VAL* 1.3 63.1 + - - +
206C PRO* 3.0 8.4 - - - +
207C ASN 3.0 12.1 + - - -
208C TRP* 2.8 41.3 + - - -
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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