Contacts of the helix formed by residues 28 - 40 (chain A) in PDB entry 1C3Q
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 VAL 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 3.6 13.2 - - + +
25A ASN* 3.4 29.2 - - - +
27A VAL* 1.3 85.7 - - - +
29A THR* 1.3 59.1 + - - +
30A ASN 3.4 2.5 - - - -
31A PHE* 3.3 5.0 + - + -
32A THR* 2.8 37.1 + - - +
194A THR* 4.2 3.6 - - - +
195A GLY* 3.3 36.8 - - - +
198A CYS* 3.6 16.6 - - + -
302A TZE 3.9 15.5 - - + -
30B ASN* 4.2 5.6 - - - +
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Residues in contact with THR 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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24A THR* 3.9 14.4 - - + +
25A ASN 3.5 17.3 + - - +
26A ASN* 4.1 10.0 + - - -
27A VAL 3.8 0.6 - - - -
28A VAL* 1.3 75.7 - - - +
30A ASN* 1.3 60.1 + - - +
32A THR* 3.7 5.8 - - - -
33A ALA* 3.0 30.7 + - - +
45A MET* 4.7 4.3 - - + +
47A TYR* 3.3 26.7 - - + +
26C ASN* 2.7 36.4 + - - +
27C VAL* 3.7 13.4 - - + +
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Residues in contact with ASN 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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28A VAL 3.4 0.6 - - - -
29A THR* 1.3 78.7 + - - +
31A PHE* 1.3 62.2 + - - +
33A ALA 3.4 0.3 + - - -
34A ASN* 2.9 54.9 + - - +
30B ASN* 5.7 10.0 - - + +
27C VAL* 2.8 29.9 + - - +
28C VAL* 4.4 1.0 - - - +
30C ASN* 6.0 6.0 - - + +
31C PHE* 4.2 25.3 - - - +
194C THR* 3.2 19.5 + - - +
245C GLN* 4.5 6.9 - - - +
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Residues in contact with PHE 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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28A VAL* 3.3 8.7 + - - +
30A ASN* 1.3 80.0 + - - +
32A THR* 1.3 58.5 + - - +
34A ASN* 3.8 2.4 - - - -
35A GLY* 2.8 28.6 + - - -
193A VAL* 4.0 13.7 - - + -
194A THR 3.6 20.0 - - - +
195A GLY* 3.9 22.0 - - - -
196A ALA* 4.1 6.3 - - - -
199A LEU* 3.6 26.8 - - + +
225A TYR* 4.6 0.2 - - - -
245A GLN* 3.5 35.4 - - + +
248A LEU* 4.1 17.7 - - + -
249A LEU* 3.8 25.4 - - + -
30B ASN* 4.3 21.0 - - - +
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Residues in contact with THR 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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22A SER* 4.6 14.8 - - - +
24A THR* 4.9 5.6 + - + +
28A VAL* 2.8 37.9 + - - +
29A THR* 3.7 5.8 - - - -
31A PHE* 1.3 77.4 - - - +
33A ALA* 1.3 64.0 + - - +
36A LEU* 3.0 33.4 + - + +
45A MET* 5.4 4.5 - - - -
195A GLY 5.2 0.2 + - - -
198A CYS* 4.4 1.0 - - - +
199A LEU* 3.6 22.2 + - + +
202A SER* 3.3 32.0 + - - +
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Residues in contact with ALA 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 THR 3.0 18.0 + - - +
30A ASN 3.9 0.7 - - - +
32A THR* 1.3 76.2 - - - +
34A ASN* 1.3 58.2 + - - +
36A LEU 3.4 0.7 + - - -
37A LEU* 3.0 33.8 + - - +
43A PRO* 3.6 24.8 - - + +
45A MET* 4.2 9.9 - - + -
27C VAL* 3.7 11.2 - - + -
194C THR* 3.6 24.9 - - - +
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Residues in contact with ASN 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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30A ASN* 2.9 41.8 + - - +
31A PHE* 3.9 3.5 - - - +
33A ALA* 1.3 73.5 - - - +
35A GLY* 1.3 61.2 + - - +
37A LEU* 3.4 5.0 + - - +
38A ALA* 3.0 30.1 + - - +
249A LEU* 4.0 19.0 - - + +
192C LYS 4.0 4.0 - - - +
193C VAL* 3.5 12.2 - - - +
194C THR* 2.8 36.5 + - - +
245C GLN* 3.6 23.8 + - - +
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Residues in contact with GLY 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 PHE 2.8 17.8 + - - -
34A ASN* 1.3 77.9 - - - +
36A LEU* 1.3 60.4 + - - +
38A ALA* 3.4 3.0 + - - +
39A LEU* 3.0 24.1 + - - +
199A LEU* 3.7 21.1 - - - -
203A VAL* 5.6 0.6 - - - +
249A LEU* 3.6 16.8 - - - +
252A LEU* 4.0 8.2 - - - +
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Residues in contact with LEU 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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20A VAL* 4.1 20.0 - - + +
22A SER* 5.8 2.2 - - - -
32A THR* 3.0 24.8 + - + +
33A ALA 3.8 4.0 - - - +
35A GLY* 1.3 74.1 - - - +
37A LEU* 1.3 64.3 + - - +
39A LEU* 3.3 7.9 + - + +
40A GLY 3.0 5.2 + - - -
41A ALA* 2.9 45.5 + - + -
43A PRO* 3.7 29.2 - - + -
45A MET* 6.2 0.2 - - - -
199A LEU* 4.0 2.0 - - + +
202A SER* 3.8 42.6 - - - +
203A VAL* 4.4 7.0 - - + +
206A ALA* 4.1 10.1 - - + -
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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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33A ALA 3.0 21.1 + - - +
34A ASN* 3.8 2.9 - - - +
36A LEU* 1.3 75.8 - - - +
38A ALA* 1.3 65.4 + - - +
40A GLY* 3.1 14.2 + - - -
41A ALA 3.7 9.4 - - - +
42A SER* 5.0 1.3 - - - +
43A PRO* 3.6 23.6 - - + -
301A TZE 6.4 0.9 - - + -
191C THR 3.7 16.6 - - - +
192C LYS* 3.7 36.1 - - + +
193C VAL 3.7 7.9 - - - +
194C THR* 3.3 38.1 - - - +
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Residues in contact with ALA 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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14A ARG* 5.3 0.2 + - - -
34A ASN 3.0 17.6 + - - +
35A GLY 3.7 4.7 - - - +
37A LEU* 1.3 77.5 - - - +
39A LEU* 1.3 63.6 + - - +
40A GLY* 3.3 1.0 + - - -
249A LEU* 3.2 32.5 - - + +
252A LEU* 3.9 7.6 - - + -
253A SER* 3.2 22.3 + - - -
192C LYS* 4.7 2.7 + - - +
241C PRO* 3.7 23.3 - - + -
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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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10A LEU* 3.8 26.0 - - + -
13A VAL* 4.1 21.4 - - + +
14A ARG* 3.2 30.8 + - - +
35A GLY 3.0 17.9 + - - +
36A LEU* 3.5 9.4 - - + +
37A LEU 3.2 0.2 - - - -
38A ALA* 1.3 76.7 - - - +
40A GLY* 1.3 57.6 + - - +
41A ALA* 4.8 1.8 - - + -
203A VAL* 3.9 32.1 - - + -
206A ALA* 4.2 11.7 - - + -
207A PHE* 4.1 10.1 - - + -
224A SER* 5.7 3.4 - - - -
252A LEU* 3.4 32.5 + - + +
255A VAL* 5.8 1.3 - - + -
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Residues in contact with GLY 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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13A VAL* 3.9 8.8 - - - +
14A ARG* 4.4 12.3 - - - +
17A SER* 3.1 27.1 + - - -
36A LEU 3.0 2.6 + - - -
37A LEU 3.1 11.0 + - - -
38A ALA 4.2 0.7 - - - -
39A LEU* 1.3 80.5 - - - +
41A ALA* 1.3 62.7 + - - +
192C LYS* 6.1 2.7 - - - -
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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