Contacts of the helix formed by residues 37 - 49 (chain D) in PDB entry 2P5L
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 THR 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B G 2.8 62.1 + - + +
5B A 3.5 15.5 - - + +
26D VAL* 3.8 8.3 - - - -
30D LYS* 5.3 2.7 - - - +
36D VAL* 1.3 80.6 - - - +
38D GLN* 1.3 66.4 + - - +
39D ALA* 3.9 3.8 + - - +
40D THR* 3.2 7.4 + - - -
41D VAL* 3.1 20.8 + - - +
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Residues in contact with GLN 38 (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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11A A 3.3 23.8 - - + +
12A A 2.8 50.4 + - - +
6B A 4.6 0.5 + - - -
22D GLN* 2.6 39.4 + - + +
23D ASP* 4.0 20.6 - - - +
26D VAL* 3.7 13.1 - - + +
37D THR* 1.3 72.0 - - - +
39D ALA* 1.3 69.4 + - - +
41D VAL* 2.8 3.2 + - - -
42D SER* 2.8 21.5 + - - -
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Residues in contact with ALA 39 (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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13A T 3.3 30.4 - - - +
4B G 3.8 15.0 - - + +
5B A 3.7 18.8 - - - +
6B A 4.2 4.5 - - - +
37D THR* 3.9 5.7 + - - +
38D GLN* 1.3 85.7 + - - +
40D THR* 1.3 66.3 + - - +
42D SER* 3.1 3.7 + - - -
43D ARG* 3.0 29.3 + - - +
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Residues in contact with THR 40 (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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3B T 3.2 27.1 + - - +
4B G 2.8 25.3 + - - +
6D ARG* 3.4 26.0 - - - +
36D VAL* 3.6 13.9 - - + -
37D THR* 3.2 6.9 + - - -
38D GLN 3.2 0.4 - - - -
39D ALA* 1.3 80.8 - - - +
41D VAL* 1.3 57.5 + - - +
43D ARG* 3.2 13.2 + - - +
44D ASP* 2.7 46.9 + - - +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 5.1 2.9 - - + -
22D GLN* 4.0 12.8 - - + -
25D LEU* 3.7 17.9 - - + -
26D VAL* 3.6 27.8 - - + +
29D LEU* 4.0 25.4 - - + -
36D VAL* 4.7 7.2 - - + -
37D THR 3.1 6.0 + - - +
38D GLN* 2.8 8.7 + - - +
40D THR* 1.3 73.5 - - + +
42D SER* 1.3 57.2 + - - +
44D ASP* 3.1 6.9 + - + +
45D ILE* 2.6 57.0 + - + +
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A A 2.9 50.0 + - - +
13A T 3.8 7.4 - - - +
60C TYR* 3.9 3.8 + - - -
22D GLN* 3.5 23.3 + - - +
38D GLN* 2.8 13.2 + - - -
39D ALA 3.4 8.5 - - - -
41D VAL* 1.3 71.4 - - - +
43D ARG* 1.3 58.7 + - - +
45D ILE* 3.2 4.0 + - - +
46D LYS* 2.8 29.2 + - - +
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Residues in contact with ARG 43 (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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13A T 4.3 15.1 - - + +
14A T 2.6 26.3 + - - +
15A C 4.0 3.6 - - - +
3B T 3.3 41.9 - - - +
4B G 2.5 41.3 + - - -
5B A 3.8 2.6 - - - +
39D ALA* 3.0 14.3 + - - +
40D THR* 3.5 22.8 + - + +
42D SER* 1.3 77.0 - - - +
44D ASP* 1.3 56.6 + - - +
46D LYS* 3.0 9.0 + - + +
47D GLU* 2.7 49.7 + - + +
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Residues in contact with ASP 44 (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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3B T 4.5 0.5 + - - -
3D LYS* 4.5 0.2 - - - +
6D ARG* 2.6 43.7 + - - -
7D HIS* 2.8 33.1 + - - +
10D ILE* 3.1 24.6 - - + +
40D THR* 2.7 32.5 + - - +
41D VAL* 3.4 6.7 - - - +
43D ARG* 1.3 72.1 - - - +
45D ILE* 1.3 57.8 + - - +
47D GLU* 3.2 5.6 + - - +
48D LEU* 2.8 37.3 + - - +
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Residues in contact with ILE 45 (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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12A A 4.8 2.2 - - - +
54C PRO* 3.7 2.5 - - + +
60C TYR* 4.7 9.0 - - + +
10D ILE* 5.3 1.3 - - + -
22D GLN* 3.6 17.3 - - + +
25D LEU* 4.2 10.1 - - + -
41D VAL* 2.6 43.4 + - + +
42D SER* 3.5 5.6 - - - +
44D ASP* 1.3 74.4 - - + +
46D LYS* 1.3 62.1 + - - +
48D LEU* 3.4 1.1 + - - -
49D HIS* 3.0 22.7 + - - -
50D LEU* 3.0 42.4 + - + +
51D VAL* 5.6 0.2 - - - -
62D TYR* 3.5 39.7 - - + -
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Residues in contact with LYS 46 (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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12A A 5.4 0.4 - - + -
13A T 2.9 34.5 + - - +
54C PRO* 3.3 21.9 - - + +
58C GLY* 3.1 36.4 + - - -
59C SER* 4.4 2.0 - - - +
60C TYR* 3.2 37.7 - - + +
42D SER* 2.8 13.2 + - - +
43D ARG* 3.0 8.9 + - - +
45D ILE* 1.3 75.6 - - - +
47D GLU* 1.3 66.6 + - + +
49D HIS* 3.2 20.6 + - - -
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Residues in contact with GLU 47 (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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3D LYS* 2.6 45.3 + - - +
7D HIS* 3.4 19.8 + - + -
43D ARG* 2.7 37.7 + - + +
44D ASP* 3.9 7.5 - - - +
46D LYS* 1.3 75.7 - - + +
48D LEU* 1.3 63.5 + - - +
49D HIS* 3.4 11.6 + - - -
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Residues in contact with LEU 48 (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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7D HIS* 3.8 52.7 - - + +
10D ILE* 4.3 19.5 - - + -
11D ARG* 3.2 41.4 + - + +
44D ASP 2.8 19.8 + - - +
47D GLU* 1.3 80.1 - - - +
49D HIS* 1.3 68.9 + - - +
50D LEU* 3.3 25.1 + - + +
64D LEU* 5.6 1.6 - - - +
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Residues in contact with HIS 49 (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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53C VAL* 4.7 6.6 - - + +
54C PRO* 3.2 32.1 + - + +
55C THR* 3.4 24.0 + - - -
56C ASN* 3.1 28.6 + - - -
45D ILE 3.0 4.0 + - - -
46D LYS 3.2 14.4 + - - -
47D GLU* 3.4 10.6 + - - -
48D LEU* 1.3 79.4 - - - +
50D LEU* 1.3 68.0 + - - +
51D VAL* 3.8 9.4 + - - +
64D LEU* 4.7 6.9 - - - +
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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