Contacts of the helix formed by residues 10 - 25 (chain D) in PDB entry 3P9I
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 ALA 10 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PRO* 5.6 4.3 - - + -
231B HIS* 5.3 17.0 - - + +
187C LYS* 4.6 8.1 - - - +
350C TYR* 3.3 25.2 + - - -
11D SER* 1.3 54.4 + - - +
12D ALA* 4.2 5.6 - - + +
13D ASP* 3.0 21.1 + - + +
14D GLU* 2.4 41.3 + - - +
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Residues in contact with SER 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PRO 5.1 1.0 + - - -
231B HIS* 5.9 0.8 - - - +
234B SER* 3.2 37.0 + - - -
10D ALA* 1.3 72.1 - - - +
12D ALA* 1.3 54.6 + - - +
14D GLU* 4.1 10.1 - - - -
15D ASP* 2.5 50.8 + - - +
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PRO* 4.4 25.5 + - + +
10D ALA* 3.1 3.7 - - + +
11D SER* 1.3 79.6 - - - +
13D ASP* 1.3 58.6 + - - +
15D ASP* 3.2 9.1 + - - +
16D ALA* 3.0 26.9 + - - +
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Residues in contact with ASP 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 3.9 19.3 + - - -
111C PHE* 2.9 32.4 - - + -
350C TYR* 3.5 11.4 - - - +
10D ALA* 3.0 22.3 + - + +
12D ALA* 1.3 78.7 - - - +
14D GLU* 1.3 61.8 + - - +
16D ALA* 3.2 2.3 + - - -
17D CYS* 2.8 24.4 + - - +
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C TYR* 2.6 40.9 + - - -
350C TYR* 3.2 31.6 + - + -
351C ALA 2.8 16.7 + - - +
10D ALA 2.4 32.1 + - - +
11D SER* 3.7 8.5 - - - +
13D ASP* 1.3 65.6 - - - +
15D ASP* 1.3 57.6 + - - +
17D CYS* 3.2 0.7 + - - +
18D MET* 2.7 59.5 + - + +
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Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO* 5.7 1.2 - - - +
11D SER* 2.5 40.1 + - - +
12D ALA* 3.4 7.0 - - - +
13D ASP 3.2 0.2 - - - -
14D GLU* 1.3 79.5 - - - +
16D ALA* 1.3 57.2 + - - +
18D MET* 3.8 20.4 - - - +
19D PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PRO* 4.3 25.1 - - + +
108C VAL* 3.5 10.7 - - - +
110C LYS* 4.3 6.7 - - - +
111C PHE* 3.4 23.8 - - + -
12D ALA 3.0 13.4 + - - +
13D ASP 3.2 2.4 + - - +
15D ASP* 1.3 75.1 - - - +
17D CYS* 1.3 60.6 + - - +
19D PHE* 3.2 8.8 + - - +
20D ALA* 2.9 24.3 + - - +
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Residues in contact with CYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C PHE* 3.2 32.3 - - + -
121C MET* 3.7 29.8 - - - -
183C ILE* 4.9 6.1 - - - -
350C TYR* 4.2 17.5 - - + -
351C ALA* 4.1 15.9 - - + -
13D ASP 2.8 19.6 + - - +
14D GLU 3.2 4.2 + - - +
16D ALA* 1.3 73.6 - - - +
18D MET* 1.3 57.8 + - - +
20D ALA* 3.2 3.1 + - - +
21D LEU* 2.9 26.7 + - - +
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO* 4.7 17.9 - - + +
306C SER* 4.1 30.3 - - - +
348C TYR* 4.3 10.5 - - - -
351C ALA* 3.9 19.1 - - - -
352C ASN* 4.2 15.0 - - - +
14D GLU* 2.7 44.0 + - + +
15D ASP* 3.8 22.4 - - - +
17D CYS* 1.3 72.5 - - - +
19D PHE* 1.3 63.1 + - - +
21D LEU* 3.2 11.1 + - - +
22D GLN* 3.0 23.8 + - - +
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TYR* 3.4 21.8 - + + -
85C ASN* 3.9 23.6 - - + -
86C VAL* 4.6 0.9 - - + -
108C VAL* 3.6 22.9 - - + -
305C PRO* 4.9 8.5 - - + +
15D ASP 2.9 18.6 + - - +
16D ALA* 3.4 6.7 - - - +
18D MET* 1.3 78.9 - - - +
20D ALA* 1.3 61.0 + - - +
22D GLN* 3.3 22.1 + - - +
23D LEU* 3.0 54.6 + - + +
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 3.5 17.0 - - + +
111C PHE* 3.7 30.7 - - + +
112C LEU* 4.1 12.2 - - + +
121C MET* 4.2 6.3 - - + -
16D ALA 2.9 13.6 + - - +
17D CYS 3.2 8.5 + - - +
19D PHE* 1.3 77.2 - - - +
21D LEU* 1.3 56.3 + - - +
23D LEU* 3.3 6.7 + - - +
24D ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C MET* 3.5 37.0 - - + -
124C LEU* 4.0 12.3 - - + -
180C HIS* 4.0 15.3 - - + +
263C TRP* 5.5 1.6 - - + -
309C GLY* 6.0 1.1 - - - -
351C ALA* 3.4 44.0 - - + +
603C SNY 4.9 6.2 - - - +
3295C BME 3.9 22.7 - - - +
17D CYS 2.9 14.7 + - - +
18D MET* 3.2 10.3 + - + +
20D ALA* 1.3 78.1 - - - +
22D GLN* 1.3 61.0 + - - +
24D ALA* 3.3 14.0 + - - +
25D SER* 3.4 14.4 + - - -
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO* 3.5 32.5 - - - +
308C GLN* 2.8 33.5 + - - +
309C GLY* 4.9 7.3 - - - +
312C HIS* 3.4 26.2 - - + -
18D MET 3.0 14.8 + - - +
19D PHE* 3.6 22.4 - - + +
20D ALA 3.3 0.2 - - - -
21D LEU* 1.3 77.4 - - - +
23D LEU* 1.3 63.6 + - + +
25D SER* 3.3 3.0 + - - -
26D SER* 3.2 19.1 + - - -
84D TYR* 3.0 20.1 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 3.9 37.5 - - + -
30C PRO* 4.9 0.9 - - - +
33C LEU* 3.7 22.4 - - + +
84C TYR* 5.7 0.4 - - + -
86C VAL* 3.9 22.9 - - + -
108C VAL* 4.1 14.1 - - + -
112C LEU* 4.1 13.2 - - + -
129C GLN* 4.7 2.9 + - - -
19D PHE* 3.0 52.2 + - + +
20D ALA* 3.6 4.3 - - - +
22D GLN* 1.3 74.0 - - + +
24D ALA* 1.3 61.3 + - - +
25D SER 3.0 5.4 - - - -
26D SER* 2.8 23.9 + - - -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 5.1 0.2 - - - -
112C LEU* 5.3 1.1 - - + +
121C MET* 3.6 14.6 - - + +
124C LEU* 4.0 9.9 - - + -
125C ALA* 3.4 34.8 - - + +
128C ASN* 3.1 13.6 + - - +
129C GLN* 2.9 21.2 + - - -
603C SNY 5.1 1.1 - - - +
20D ALA 2.9 16.4 + - - +
21D LEU* 3.7 9.6 - - - +
22D GLN 3.3 0.4 - - - -
23D LEU* 1.3 75.1 - - - +
25D SER* 1.3 57.8 + - - +
26D SER 3.7 0.2 - - - -
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ASN* 3.6 19.7 - - - +
129C GLN* 4.0 4.0 - - - -
309C GLY* 5.7 0.3 - - - -
312C HIS* 2.8 35.1 + - - +
313C VAL* 5.3 1.6 - - - +
316C ILE* 3.7 19.3 - - - -
603C SNY 3.8 6.8 + - - -
21D LEU 3.4 10.2 + - - -
22D GLN* 3.3 2.5 + - - -
23D LEU 3.0 0.4 - - - -
24D ALA* 1.3 78.9 - - - +
26D SER* 1.3 56.3 + - - +
27D SER* 3.1 11.9 + - - -
28D VAL* 3.2 19.8 + - - +
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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