Contacts of the helix formed by residues 37 - 48 (chain B) in PDB entry 2POD
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 GLY 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 6.6 0.4 - - - -
47A GLU* 3.3 20.1 + - - -
80A GLU* 5.6 0.2 - - - -
16B ASN* 4.3 7.9 - - - +
36B TYR* 1.3 73.1 - - - +
38B ALA* 1.3 64.4 + - - +
40B SER* 2.8 21.7 + - - -
41B ALA* 3.0 8.7 + - - +
82B ARG* 3.1 14.1 + - - -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.1 5.4 + - - +
10B ARG* 4.0 14.4 - - + -
15B PRO 3.6 21.7 + - - +
16B ASN 3.8 7.6 + - - +
17B LEU 3.7 20.2 - - - +
18B LEU* 3.9 15.4 - - + +
34B THR* 6.0 0.2 - - - -
36B TYR 3.3 3.7 + - - -
37B GLY* 1.3 74.9 - - - +
39B CYS* 1.3 57.8 + - - +
41B ALA* 3.8 2.4 - - - -
42B GLU* 2.9 32.1 + - - +
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Residues in contact with CYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.4 13.5 - - + +
47A GLU* 3.1 36.3 + - + +
10B ARG* 3.6 40.4 - - - +
38B ALA* 1.3 76.9 - - - +
40B SER* 1.3 57.9 + - - +
42B GLU* 3.9 4.3 - - - +
43B ALA* 3.0 28.6 + - - +
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A SER* 3.4 30.0 - - - -
43A ALA* 3.8 7.6 - - - -
44A TYR* 3.9 21.3 - - - +
47A GLU* 3.5 2.9 + - - -
79A ALA* 5.0 0.2 - - - -
80A GLU* 4.2 3.9 + - - +
37B GLY* 2.8 21.7 + - - -
39B CYS* 1.3 75.5 - - - +
41B ALA* 1.3 60.6 + - - +
44B TYR* 3.0 24.9 + - - +
79B ALA* 3.5 12.6 - - - +
82B ARG* 3.2 13.0 + - - -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.9 19.3 - - + -
34B THR* 4.3 9.9 - - + -
36B TYR 5.1 0.2 - - - +
37B GLY 3.0 15.2 + - - +
38B ALA* 3.9 1.1 - - - +
40B SER* 1.3 75.0 + - - +
42B GLU* 1.3 64.0 + - - +
44B TYR* 3.4 4.7 + - - +
45B ILE* 3.1 27.2 + - - +
79B ALA* 3.8 21.7 - - - +
82B ARG* 4.3 8.7 - - + +
83B GLY* 4.2 10.8 - - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 2.6 39.5 + - - +
10B ARG* 2.7 43.0 + - - +
18B LEU* 3.8 15.1 - - + +
38B ALA 2.9 22.0 + - - +
39B CYS* 3.9 5.5 - - - +
41B ALA* 1.3 72.6 - - - +
43B ALA* 1.3 63.3 + - - +
45B ILE* 3.2 3.4 + - - +
46B HIS* 3.2 36.0 + - + -
393B ALA 4.3 4.3 - - - +
394B VAL 4.9 0.2 - - - -
395B ARG* 3.9 24.4 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 3.5 35.3 - - + +
40A SER* 4.4 1.6 - - - -
43A ALA* 3.8 6.7 - - + -
39B CYS 3.0 19.7 + - - +
40B SER 3.8 2.7 - - - +
41B ALA 3.4 0.2 - - - -
42B GLU* 1.3 76.2 - - - +
44B TYR* 1.3 57.4 + - - +
46B HIS* 3.6 1.2 + - - +
47B GLU* 2.9 32.9 + - - +
395B ARG* 3.8 18.1 + - - +
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY* 6.6 0.2 - - - -
40A SER* 3.8 16.7 - - - -
40B SER 3.0 17.5 + - - +
41B ALA* 3.5 7.6 - - - +
43B ALA* 1.3 74.7 - - - +
45B ILE* 1.3 67.4 + - - +
47B GLU* 4.4 4.3 - - - -
48B TRP* 3.1 61.9 + + + -
49B ALA* 3.5 15.0 + - + +
68B LEU 3.4 4.2 + - - -
79B ALA 4.0 7.4 - - - +
80B GLU* 3.3 52.2 - - + +
83B GLY* 4.0 6.3 - - - -
84B ASN* 2.5 40.6 + - - -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.9 27.4 - - + -
8B THR* 4.2 15.5 - - + -
18B LEU* 4.4 6.1 - - + -
20B VAL* 3.7 30.7 - - + -
41B ALA 3.1 19.8 + - - +
42B GLU 3.2 7.2 + - - +
44B TYR* 1.3 77.5 - - + +
46B HIS* 1.3 65.3 + - - +
49B ALA* 3.3 6.6 + - - -
50B ALA* 2.8 35.6 + - + +
83B GLY* 4.0 25.1 - - - +
87B LEU* 3.9 23.6 - - + -
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE 3.9 5.4 - - - -
8B THR* 2.7 37.4 + - + +
42B GLU* 3.2 32.4 + - + +
43B ALA 4.3 1.6 - - - +
45B ILE* 1.3 79.7 - - + +
47B GLU* 1.3 62.3 + - - +
48B TRP 3.5 0.2 - - - -
50B ALA* 4.3 7.4 - - - +
51B ASN* 4.4 10.0 + - - -
395B ARG* 3.5 60.0 - - + +
396B ASN 3.9 3.1 + - - -
397B THR* 3.3 34.0 + - + +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO 4.4 5.9 - - - +
16A ASN* 5.7 1.2 + - - -
37A GLY* 3.4 18.7 + - - -
38A ALA* 3.1 15.2 + - - +
39A CYS* 2.9 51.9 + - + +
40A SER* 3.5 8.0 + - - -
43B ALA 2.9 18.5 + - - +
44B TYR* 3.3 4.9 + - - +
46B HIS* 1.3 78.4 - - - +
48B TRP* 1.3 62.6 + - + +
51B ASN* 4.0 11.0 + - - -
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Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 3.1 47.4 + + + +
46B HIS 3.5 0.6 - - - -
47B GLU* 1.3 85.8 - - + +
49B ALA* 1.3 67.3 + - - +
50B ALA 3.4 2.5 + - - -
51B ASN* 3.7 12.6 + - - +
52B ARG* 3.6 40.5 + - + +
67B ARG 3.5 21.5 - - - -
68B LEU* 3.4 26.0 - - + -
70B GLY* 4.0 20.0 - - - -
71B TYR 5.6 0.4 - - - -
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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