Contacts of the helix formed by residues 15 - 28 (chain D) in PDB entry 3OQN
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 HIS 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292C VAL* 6.4 2.0 - - + -
294C PRO* 4.3 13.4 - - + +
297C ASP* 2.7 34.4 + - + +
323C PRO* 5.4 5.8 - - + -
325C ARG* 5.5 7.6 + - - -
12D SER* 3.5 26.9 - - - +
13D GLY 3.4 5.2 + - - +
14D ILE* 1.3 82.1 + - - +
16D ALA* 1.3 76.8 + - + +
18D PRO* 3.5 5.5 - - - +
19D ALA* 2.9 21.8 + - - +
51D MET* 4.7 7.6 - - - -
54D GLY* 4.0 19.1 - - - -
55D ILE 3.0 26.6 + - - -
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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
----------------------------------------------------------
78C GLU* 5.1 4.7 - - - +
296C TYR* 3.3 38.5 - - + -
297C ASP* 3.3 10.3 + - - -
12D SER* 5.9 3.1 - - - +
15D HIS* 1.3 86.1 - - + +
17D ARG* 1.3 77.9 + - - +
18D PRO* 3.8 7.9 - - + -
19D ALA* 3.4 9.4 - - - +
20D THR* 3.4 2.1 + - - -
51D MET* 4.5 0.9 - - - +
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 4.6 2.6 + - - -
72A SER* 3.4 23.8 + - - -
78C GLU* 3.7 18.0 + - - -
81C ARG* 3.7 32.1 - - - +
85C ASP* 3.9 8.7 - - - +
296C TYR* 3.4 29.4 - - + +
16D ALA* 1.3 86.5 - - - +
18D PRO* 1.3 61.7 - - + +
20D THR* 2.6 27.4 + - - -
21D VAL* 2.7 19.0 + - + +
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Residues in contact with PRO 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 6.0 2.2 - - - +
13D GLY 5.3 2.0 - - - +
15D HIS 3.5 6.1 - - - +
16D ALA* 3.4 11.7 - - + -
17D ARG* 1.3 95.6 - - + +
19D ALA* 1.3 51.0 + - - +
21D VAL* 2.8 24.2 + - + +
22D LEU* 2.8 18.7 + - - +
84D GLU* 3.6 36.6 - - + +
86D LEU* 3.8 22.4 - - + +
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.7 20.4 - - + +
15D HIS* 2.9 41.4 + - - +
16D ALA 3.4 2.5 - - - +
18D PRO* 1.3 76.2 - - - +
20D THR* 1.3 63.7 + - - +
22D LEU* 3.3 6.1 + - - +
23D VAL* 3.0 31.3 + - - +
50D VAL* 5.2 1.3 - - + -
51D MET* 4.2 15.5 - - + -
86D LEU* 4.5 1.9 - - - +
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Residues in contact with THR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 5.4 4.5 - - + +
86C ILE* 4.0 6.9 - - + +
89C MET* 3.8 18.6 - - + -
296C TYR* 3.2 35.9 + - - +
16D ALA 3.4 0.4 + - - -
17D ARG* 2.6 18.0 + - - -
19D ALA* 1.3 75.9 - - - +
21D VAL* 1.3 54.7 + - + -
23D VAL* 3.6 0.9 + - - +
24D GLN* 2.8 58.9 + - - +
47D ILE* 4.1 9.4 - - + -
51D MET* 3.9 7.8 - - - +
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ARG* 2.7 22.8 + - + +
18D PRO* 2.8 18.6 + - + +
20D THR* 1.3 74.5 - - - +
22D LEU* 1.3 62.0 + - - +
24D GLN* 3.5 11.6 + - - +
25D THR* 2.8 27.9 + - - +
80D THR* 3.8 25.4 - - + +
84D GLU* 4.0 25.8 - - + +
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Residues in contact with LEU 22 (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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14D ILE* 4.4 21.5 - - + -
18D PRO 2.8 13.2 + - - +
19D ALA* 3.6 7.9 - - - +
21D VAL* 1.3 73.4 - - - +
23D VAL* 1.3 64.5 + - - +
25D THR* 2.9 19.7 + - - -
26D ALA 3.2 8.7 + - - -
35D LEU* 4.9 4.3 - - + -
44D LEU* 3.5 28.3 - - + +
50D VAL* 5.5 1.6 - - + -
61D ILE* 5.6 0.4 - - + -
63D ILE* 4.4 7.0 - - + -
77D LEU* 3.4 32.5 - - + +
80D THR* 4.3 6.5 - - - +
81D MET* 3.2 49.1 - - + -
86D LEU* 4.7 1.6 - - + -
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Residues in contact with VAL 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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89C MET* 5.4 2.0 - - - -
19D ALA* 3.0 23.3 + - + +
20D THR 3.9 0.4 - - - +
22D LEU* 1.3 76.5 - - + +
24D GLN* 1.3 60.6 + - + +
26D ALA 3.4 0.7 + - - -
27D SER* 3.0 23.9 + - - +
44D LEU* 3.1 29.5 - - + +
45D LYS 3.7 10.3 - - - +
47D ILE* 3.5 50.7 - - + +
50D VAL* 3.8 31.0 - - + -
51D MET* 5.4 0.9 - - + -
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Residues in contact with GLN 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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85C ASP 5.0 2.2 + - - -
89C MET* 3.3 49.0 - - + +
20D THR* 2.8 39.8 + - + +
21D VAL* 3.7 11.2 - - - +
23D VAL* 1.3 71.0 - - + +
25D THR* 1.3 66.3 + - - +
26D ALA 3.1 2.0 - - - -
27D SER* 2.9 21.6 + - - -
28D LYS* 3.1 16.7 + - - +
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Residues in contact with THR 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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21D VAL* 2.8 19.6 + - - +
22D LEU 2.9 8.9 + - - -
24D GLN* 1.3 75.1 - - - +
26D ALA* 1.3 62.2 + - - +
28D LYS* 3.1 34.1 - - + +
29D TYR* 3.4 8.9 - - + -
76D ALA* 3.9 15.7 - - + +
77D LEU* 3.8 31.2 - - + +
80D THR* 3.3 31.0 + - + +
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Residues in contact with ALA 26 (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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22D LEU 3.2 1.6 + - - -
23D VAL 3.5 8.5 - - - +
24D GLN 3.1 0.6 - - - -
25D THR* 1.3 76.9 - - - +
27D SER* 1.3 60.2 + - - +
28D LYS 3.0 6.4 + - - -
29D TYR* 3.2 14.5 + - - +
33D VAL* 3.8 27.2 - - + +
44D LEU* 3.5 27.1 - - + +
45D LYS* 3.1 29.6 - - + +
77D LEU* 4.1 6.3 - - + -
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET* 5.9 2.9 - - - -
23D VAL* 3.0 16.1 + - - +
24D GLN* 2.9 14.0 + - - -
26D ALA* 1.3 75.7 - - - +
28D LYS* 1.3 62.7 + - - +
29D TYR 3.1 5.2 + - - +
45D LYS* 3.5 29.1 + - - +
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Residues in contact with LYS 28 (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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24D GLN* 3.1 13.5 + - - +
25D THR* 3.1 28.9 - - + +
26D ALA 3.0 0.6 - - - -
27D SER* 1.3 79.7 - - - +
29D TYR* 1.3 78.1 + - + +
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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
------------------------------------------------------------
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