Contacts of the helix formed by residues 24 - 43 (chain A) in PDB entry 1AB3
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 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER* 1.3 80.2 + - - +
25A GLU* 1.3 65.6 + - + +
27A GLN* 3.6 6.1 - - - +
28A VAL* 3.0 31.3 + - + +
61A GLN* 4.5 11.9 - - - +
65A LEU* 6.4 0.2 - - + -
68A TYR* 5.2 17.4 - - + -
69A LEU* 6.1 6.5 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 5.6 1.1 - - - -
16A ARG* 3.1 27.1 + - - +
23A SER* 3.3 7.9 + - - +
24A THR* 1.3 77.0 - - + +
26A VAL* 1.3 72.0 + - + +
27A GLN 2.9 2.5 + - - -
28A VAL* 2.9 19.3 + - - +
29A ALA* 3.2 9.2 + - - +
69A LEU* 3.8 18.8 - - + +
76A ARG* 3.3 29.9 + - - -
80A LEU* 3.2 48.4 - - + +
84A LEU* 4.9 4.3 - - - +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.0 4.8 - - + +
11A ILE* 4.3 7.9 - - + +
14A PHE* 3.6 26.7 - - + +
15A ALA* 3.3 21.1 - - - +
16A ARG* 5.7 2.5 - - - +
20A ASP 2.6 27.8 - - - +
21A THR* 3.2 36.6 - - - +
23A SER* 4.0 5.1 + - - +
25A GLU* 1.3 78.0 - - + +
27A GLN* 1.3 60.7 + - - +
29A ALA* 3.2 7.1 - - - +
30A LEU* 3.2 18.3 + - + +
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Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR 4.1 7.6 - - - +
22A GLY* 3.5 16.6 + - - +
23A SER 2.6 27.6 - - - +
24A THR* 3.6 7.6 - - - +
25A GLU 3.0 0.6 - - - -
26A VAL* 1.3 74.6 - - - +
28A VAL* 1.3 59.0 + - - +
29A ALA 2.8 1.6 - - - -
30A LEU* 2.6 64.5 + - + +
31A LEU* 2.8 9.5 + - - +
61A GLN* 4.1 11.2 - - - +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.0 23.0 + - + +
25A GLU* 2.9 10.4 + - - +
27A GLN* 1.3 75.5 - - - +
29A ALA* 1.3 59.7 + - - +
31A LEU* 2.6 52.2 - - + +
32A THR* 3.5 1.6 + - - -
61A GLN* 3.6 22.9 + - - +
62A ARG* 5.2 2.7 - - + -
65A LEU* 3.0 39.5 - - + -
84A LEU* 3.9 22.3 - - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.3 0.9 - - + -
14A PHE* 2.9 51.6 - - + -
25A GLU 3.2 3.1 + - - +
26A VAL 3.2 9.6 + - - +
27A GLN 2.7 1.0 + - - -
28A VAL* 1.3 75.7 - - - +
30A LEU* 1.3 62.6 + - - +
31A LEU 2.9 5.8 + - - -
32A THR* 3.0 29.8 + - + +
33A LEU* 3.6 3.3 + - - +
84A LEU* 3.5 12.5 - - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.1 5.4 - - + -
21A THR 5.6 0.2 - - - +
26A VAL* 3.2 6.5 + - + +
27A GLN* 2.6 62.6 + - + +
29A ALA* 1.3 75.4 - - - +
31A LEU* 1.3 63.2 + - - +
32A THR 3.2 0.2 - - - -
33A LEU* 3.9 15.3 - - + +
34A ARG* 3.3 46.5 + - + +
58A MET* 5.6 1.1 - - + -
61A GLN* 5.9 0.2 - - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 2.8 4.0 + - - +
28A VAL* 2.6 40.8 - - + +
29A ALA 2.9 0.4 - - - -
30A LEU* 1.3 85.0 - - - +
32A THR* 1.3 56.7 + - - +
34A ARG 3.8 0.3 + - - -
35A ILE* 2.6 44.5 + - + +
58A MET* 3.1 36.1 - - + +
61A GLN* 2.8 43.7 - - + +
62A ARG* 3.6 30.7 - - + +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL 4.6 0.9 - - - -
29A ALA* 3.0 19.6 + - + +
31A LEU* 1.3 88.4 - - - +
33A LEU* 1.3 89.7 + - + +
35A ILE* 2.9 24.2 + - - +
36A ASN* 3.1 18.4 + - - +
62A ARG* 4.5 14.3 + - - +
84A LEU* 3.7 22.5 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.1 19.3 - - + -
29A ALA 3.6 2.0 + - - +
30A LEU* 3.5 19.2 + - + +
31A LEU 3.4 0.2 - - - -
32A THR* 1.3 90.0 - - + +
34A ARG* 1.3 61.9 + - + +
35A ILE 2.7 6.2 + - - -
36A ASN* 3.0 18.7 + - + +
37A ARG* 3.1 23.1 + - - +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.3 34.2 + - + +
31A LEU 4.1 0.4 - - - +
33A LEU* 1.3 79.5 - - + +
35A ILE* 1.3 57.3 + - - +
37A ARG* 3.9 6.8 - - - +
38A LEU* 2.9 27.7 + - - +
41A HIS* 6.4 0.2 - - - -
55A LEU* 3.9 28.6 - - + +
58A MET* 3.2 36.2 - - + +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.6 44.5 + - + +
32A THR* 2.9 17.0 + - - +
33A LEU 2.7 1.2 + - - -
34A ARG* 1.3 78.0 - - - +
36A ASN* 1.3 79.5 + - - +
38A LEU* 2.9 22.5 + - + +
39A SER* 3.6 5.9 + - - -
58A MET* 3.4 27.8 - - + -
59A VAL* 3.9 16.8 - - + +
62A ARG* 5.2 12.8 - - - +
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Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 3.1 29.1 + - - +
33A LEU* 3.0 11.6 + - + +
35A ILE* 1.3 91.1 - - - +
37A ARG* 1.3 59.9 + - + +
38A LEU 3.1 3.1 + - - -
39A SER* 3.6 10.9 + - - -
40A GLU* 3.9 17.2 + - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 5.4 16.3 - - - +
33A LEU* 3.1 23.0 + - - +
34A ARG* 3.9 6.5 - - - +
36A ASN* 1.3 76.8 - - + +
38A LEU* 1.3 58.6 + - - +
39A SER 3.5 0.2 - - - -
40A GLU* 4.1 15.1 - - + +
41A HIS* 3.1 27.2 + - + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 2.9 19.0 + - - +
35A ILE* 2.9 13.0 + - + +
37A ARG* 1.3 80.9 - - - +
39A SER* 1.3 64.9 + - - +
40A GLU 3.3 0.2 - - - -
41A HIS* 3.2 25.1 - - + +
42A LEU* 4.9 5.2 - - + +
52A HIS* 5.1 14.6 - - + -
55A LEU* 3.2 50.9 - - + +
56A LEU* 6.2 1.8 - - + -
58A MET* 4.3 6.5 - - + -
59A VAL* 4.9 13.2 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE 3.6 5.5 + - - -
36A ASN* 3.6 6.7 + - - -
38A LEU* 1.3 77.1 - - - +
40A GLU* 1.3 62.4 + - - +
41A HIS 3.1 8.8 + - - -
42A LEU* 4.5 3.9 + - - +
43A LYS* 4.1 14.4 + - - +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASN* 3.9 16.7 + - - +
37A ARG* 4.1 14.1 - - + +
38A LEU 3.3 0.8 - - - -
39A SER* 1.3 81.2 + - - +
41A HIS* 1.3 64.7 + - - +
43A LYS* 3.8 22.3 + - + +
44A VAL* 4.2 15.5 - - + +
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 6.4 0.2 - - - -
37A ARG* 3.1 19.2 + - + -
38A LEU* 3.2 21.9 - - + +
39A SER 3.1 2.6 - - - -
40A GLU* 1.3 79.1 - - - +
42A LEU* 1.3 69.2 + - + +
43A LYS 2.9 8.1 + - - -
44A VAL* 3.3 1.2 + - - +
45A HIS* 3.1 59.1 + + - +
51A SER* 5.3 12.3 - - - -
52A HIS 5.8 1.6 - - - -
55A LEU* 4.6 19.7 - - + +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.9 5.2 - - + +
39A SER 4.5 3.2 + - - +
41A HIS* 1.3 87.6 - - + +
43A LYS* 1.3 58.4 + - - +
44A VAL 3.0 10.2 + - - -
45A HIS* 4.0 19.9 + - + +
49A HIS* 5.9 5.4 - - + +
51A SER* 4.3 29.4 - - - +
52A HIS* 4.4 13.0 - - + +
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 4.1 10.0 + - - +
40A GLU* 3.8 28.9 - - + -
41A HIS 2.9 1.8 - - - -
42A LEU* 1.3 79.9 + - - +
44A VAL* 1.3 70.9 + - - +
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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
------------------------------------------------------------
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