Contacts of the helix formed by residues 37 - 49 (chain B) in PDB entry 2ABQ
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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6B THR* 3.8 16.8 - - - -
8B ASN 4.8 4.0 - - - -
9B PRO* 4.5 4.3 - - - -
10B SER* 4.3 2.9 + - - -
12B ASP* 4.2 3.6 + - - -
36B GLY* 1.3 73.2 - - - -
38B LYS* 1.3 65.8 + - - -
39B GLY 3.4 2.2 - - - -
40B ILE* 3.2 3.8 + - - +
41B ASN* 2.9 30.4 + - - +
88B ARG* 5.7 3.1 - - - -
90B ASN* 5.8 0.2 - - - +
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Residues in contact with LYS 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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6B THR* 4.4 2.6 - - - +
37B GLY* 1.3 71.2 - - - -
39B GLY* 1.3 64.0 + - - +
41B ASN* 3.2 5.0 + - - +
42B VAL* 3.0 25.7 + - - +
132B ALA* 3.7 15.5 + - + +
133B GLY* 3.7 30.1 - - - +
161B ASP* 3.4 24.9 + - - +
162B THR* 6.4 0.2 - - - +
179B LYS* 5.6 0.2 - - - +
246B GLY* 5.9 0.8 - - - -
248B GLY* 4.5 6.1 - - - +
249B ASP* 2.6 48.8 + - - +
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Residues in contact with GLY 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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4B THR* 3.6 15.6 - - - -
5B VAL 3.9 13.2 + - - -
6B THR* 3.3 16.6 + - - +
37B GLY 3.4 0.6 - - - -
38B LYS* 1.3 77.5 - - - +
40B ILE* 1.3 63.4 + - - +
42B VAL* 3.2 9.6 + - - +
43B SER* 3.1 24.1 + - - -
130B VAL* 5.5 3.1 - - - -
132B ALA* 4.5 8.5 + - - +
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Residues in contact with ILE 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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6B THR* 3.1 15.2 + - - +
9B PRO* 3.7 20.4 - - + -
35B PRO* 4.0 22.2 - - + +
36B GLY 2.9 26.2 - - - +
37B GLY 3.2 8.2 + - - +
39B GLY* 1.3 76.3 - - - +
41B ASN* 1.3 63.2 + - - +
43B SER* 3.1 10.8 + - - -
44B ARG* 3.0 32.1 + - - +
55B ALA* 5.3 3.8 - - + -
67B VAL* 3.8 24.5 - - + -
71B LEU* 4.1 12.1 - - + +
80B PHE* 4.1 17.9 - - + -
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Residues in contact with ASN 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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12B ASP* 4.8 5.9 + - - +
34B GLN* 5.3 0.5 - - - +
35B PRO 3.8 18.0 - - - +
36B GLY* 4.3 2.1 - - - -
37B GLY 2.9 25.2 + - - +
38B LYS* 3.5 1.3 - - - +
40B ILE* 1.3 76.7 - - - +
42B VAL* 1.3 58.2 + - - +
44B ARG* 3.0 8.9 + - - +
45B VAL* 2.8 34.3 + - - +
92B LYS* 6.1 0.2 - - - +
245B VAL* 5.4 4.4 - - - +
246B GLY* 4.5 8.9 - - - +
249B ASP* 2.8 34.9 + - + +
285B PHE* 3.9 26.7 - - + -
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Residues in contact with VAL 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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4B THR* 3.9 12.6 - - + -
38B LYS 3.0 17.2 + - - +
39B GLY* 3.5 9.4 - - - +
41B ASN* 1.3 75.9 - - - +
43B SER* 1.3 58.1 + - - +
46B LEU* 2.9 55.0 + - + +
130B VAL* 4.5 14.1 - - + -
132B ALA* 5.7 2.9 - - + -
249B ASP* 3.3 33.0 - - + +
252B VAL* 4.0 21.8 - - + -
253B ALA* 3.8 10.9 - - + +
256B LEU* 4.9 0.9 - - + -
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Residues in contact with SER 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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4B THR* 2.7 33.4 + - - +
39B GLY 3.1 4.5 + - - -
40B ILE* 3.1 9.9 + - - -
42B VAL* 1.3 76.0 - - - +
44B ARG* 1.3 56.8 + - - +
46B LEU* 3.4 5.6 + - - +
47B LYS* 3.0 27.5 + - - +
51B HIS 4.8 0.3 - - - +
53B THR* 3.2 23.0 + - - -
55B ALA* 3.7 8.7 - - - +
71B LEU* 6.1 1.3 - - - -
76B ILE* 3.9 20.1 - - - +
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Residues in contact with ARG 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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34B GLN* 3.1 31.8 + - - +
35B PRO* 3.2 47.2 + - - +
40B ILE* 3.0 20.5 + - - +
41B ASN* 3.0 11.8 + - - +
43B SER* 1.3 74.6 - - - +
45B VAL* 1.3 64.3 + - - +
47B LYS* 3.3 5.0 + - - +
48B ARG* 3.2 50.9 + - - +
71B LEU* 3.8 7.0 - - + -
74B GLU* 3.1 32.5 + - - +
76B ILE* 3.4 16.2 - - + -
285B PHE* 4.0 17.2 - - + -
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Residues in contact with VAL 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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41B ASN* 2.8 24.0 + - + +
42B VAL* 4.8 0.2 - - - -
44B ARG* 1.3 70.6 - - - +
46B LEU* 1.3 64.0 + - - +
48B ARG* 3.2 8.9 + - - +
49B LEU* 3.0 29.4 + - + +
246B GLY 5.1 0.4 - - - +
249B ASP 5.3 0.4 - - - -
250B SER* 3.7 23.6 - - - +
253B ALA* 3.9 21.1 - - + -
275B ALA* 5.4 0.2 - - + -
279B THR* 5.1 0.2 - - - +
285B PHE* 3.6 40.2 - - + -
286B CYS* 4.1 21.3 - - - +
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Residues in contact with LEU 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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2B ILE* 4.1 22.2 - - + -
4B THR* 4.8 0.7 - - + -
42B VAL* 2.9 43.7 + - + +
43B SER* 3.6 4.7 - - - +
45B VAL* 1.3 76.6 - - - +
47B LYS* 1.3 63.9 + - - +
49B LEU* 2.9 13.2 + - - +
50B GLY 3.1 0.3 + - - -
51B HIS* 2.9 36.5 + - + +
53B THR* 3.2 27.6 - - + -
253B ALA* 3.4 32.5 - - + +
256B LEU* 4.4 3.8 - - + -
257B ALA* 4.1 18.6 - - + +
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Residues in contact with LYS 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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43B SER 3.0 13.6 + - - +
44B ARG 3.3 10.8 - - - +
46B LEU* 1.3 76.4 - - - +
48B ARG* 1.3 64.2 + - + +
50B GLY* 3.0 14.9 + - - -
51B HIS 3.4 12.7 + - - +
52B GLU* 3.1 30.2 + - - +
74B GLU* 3.5 26.2 - - + +
75B GLU* 3.5 31.9 + - - +
76B ILE* 4.1 15.5 - - + -
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Residues in contact with ARG 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 ARG* 3.3 45.7 + - - +
45B VAL* 3.2 10.0 + - - +
47B LYS* 1.3 80.1 - - + +
49B LEU* 1.3 61.9 + - + +
50B GLY 3.2 1.1 + - - -
74B GLU* 3.9 14.5 + - - -
285B PHE* 3.0 41.1 + - - +
286B CYS 3.7 24.2 - - - +
287B THR* 5.4 4.4 - - - +
288B ARG* 4.1 15.1 + - - +
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Residues in contact with LEU 49 (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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45B VAL* 3.0 24.8 + - + +
46B LEU* 2.9 9.6 + - - +
48B ARG* 1.3 78.0 - - - +
50B GLY* 1.3 56.9 + - - +
51B HIS* 3.4 14.0 + - + -
253B ALA* 4.0 10.5 - - + +
254B GLY* 3.9 31.0 - - - +
257B ALA* 4.0 6.7 - - + -
261B GLU* 4.4 0.5 - - - +
271B PHE* 4.2 6.7 - - + -
275B ALA* 4.8 3.6 - - + -
286B CYS* 4.7 11.9 - - - +
287B THR 4.7 0.2 - - - -
288B ARG* 3.4 48.6 + - - +
291B VAL* 4.0 26.9 - - + -
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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