Contacts of the helix formed by residues 34 - 57 (chain A) in PDB entry 2AGA
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 SER 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLN* 4.3 6.6 + - - -
33A PHE* 1.3 81.1 + - - +
35A PRO* 1.4 76.0 - - - +
36A VAL* 3.3 7.4 - - - -
37A GLU* 3.6 25.4 + - - +
38A LEU* 3.4 22.3 + - - +
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Residues in contact with PRO 35 (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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18A LEU* 4.3 26.5 - - + -
21A GLN* 5.2 4.0 - - + -
34A SER* 1.4 92.4 - - - +
36A VAL* 1.3 72.9 - - + +
37A GLU 3.2 0.4 - - - -
38A LEU* 3.1 6.1 + - + -
80A PHE* 2.5 53.2 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.3 6.3 - - - -
35A PRO* 1.3 87.1 - - + +
37A GLU* 1.3 59.3 + - + +
39A SER* 3.2 9.7 + - - +
40A SER* 3.0 28.2 + - - -
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Residues in contact with GLU 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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32A TYR 5.2 3.1 - - - +
33A PHE* 4.2 25.5 - - + -
34A SER* 3.7 34.1 + - - +
35A PRO 3.2 0.2 - - - -
36A VAL* 1.3 77.2 - - + +
38A LEU* 1.3 56.3 - - - +
40A SER* 3.0 7.1 + - - -
41A ILE* 2.4 42.8 + - + +
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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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21A GLN* 3.0 58.3 - - + +
24A LEU* 4.6 2.5 - - + -
33A PHE* 5.1 3.4 - - + -
34A SER 3.4 7.5 + - - +
35A PRO 3.1 11.3 + - - +
37A GLU* 1.3 79.8 - - - +
39A SER* 1.3 52.6 + - - +
41A ILE* 3.2 14.9 - - + +
42A ALA* 2.8 36.0 + - - +
80A PHE* 3.4 33.9 - - + -
84A VAL* 3.4 35.7 - - + +
85A ILE* 4.9 1.8 - - + -
88A ALA* 5.2 0.7 - - + -
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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 PRO 3.1 6.7 + - - -
36A VAL* 3.4 10.8 - - - -
38A LEU* 1.3 78.1 - - - +
40A SER* 1.3 56.1 + - - +
43A HIS* 2.5 46.1 + - - -
74A MET* 2.7 34.9 - - - +
76A ASP* 5.1 7.1 + - - -
80A PHE* 3.2 8.1 - - - -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.0 16.2 + - - -
37A GLU* 3.6 9.0 - - - -
39A SER* 1.3 74.6 - - - +
41A ILE* 1.3 57.0 - - - +
43A HIS* 3.2 5.4 + - - +
44A GLN* 2.6 48.0 + - - +
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Residues in contact with ILE 41 (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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33A PHE* 4.1 16.8 - - + -
37A GLU* 2.4 29.5 + - + +
38A LEU* 3.2 16.4 - - + +
40A SER* 1.3 69.2 - - - +
42A ALA* 1.3 55.7 + - - +
44A GLN* 3.3 6.2 + - + +
45A LEU* 2.6 30.3 + - - +
48A GLU* 5.2 0.2 - - - +
84A VAL* 3.2 21.5 - - + +
87A ASN* 2.9 32.7 - - + +
88A ALA* 3.5 38.6 - - + +
91A VAL* 4.9 5.2 - - + -
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Residues in contact with ALA 42 (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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38A LEU 2.8 11.9 + - - +
41A ILE* 1.3 78.9 - - - +
43A HIS* 1.3 63.0 + - + +
45A LEU* 3.1 20.7 - - + +
46A ASP* 3.0 24.1 + - - +
73A ASN 4.4 2.9 - - - +
74A MET* 3.6 28.7 - - + -
81A SER* 4.3 2.5 - - - -
84A VAL* 3.1 27.1 - - + -
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Residues in contact with HIS 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* 2.5 39.3 + - - +
40A SER* 3.6 6.5 - - - +
42A ALA* 1.3 76.8 - - - +
44A GLN* 1.3 62.6 - - + +
46A ASP* 3.1 9.0 + - - +
47A GLU* 3.0 31.3 + - - +
73A ASN* 5.8 3.8 - - + +
74A MET* 2.9 36.5 - - + +
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Residues in contact with GLN 44 (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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40A SER* 2.6 30.0 + - - +
41A ILE* 3.7 7.2 - - + +
43A HIS* 1.3 73.7 - - + +
45A LEU* 1.3 52.2 + - - +
47A GLU* 4.0 11.2 - - - +
48A GLU* 2.4 78.4 + - - +
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Residues in contact with LEU 45 (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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41A ILE 2.6 9.9 + - - +
42A ALA* 3.1 25.4 - - + +
44A GLN* 1.3 71.2 - - - +
46A ASP* 1.3 62.0 + - - +
48A GLU* 4.2 7.6 - - - -
49A GLU* 2.3 62.9 + - + +
66A PHE* 4.9 6.1 - - + -
73A ASN 5.5 1.1 - - - +
81A SER* 5.1 1.1 - - - -
83A GLN* 3.1 43.3 - - + +
84A VAL* 4.9 0.2 - - + -
86A SER* 5.9 0.7 - - - -
87A ASN* 3.0 42.4 - - - +
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Residues in contact with ASP 46 (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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42A ALA 3.0 12.5 + - - +
43A HIS* 3.4 11.7 - - - +
45A LEU* 1.3 82.8 - - - +
47A GLU* 1.3 60.5 + - - +
49A GLU* 4.6 2.5 - - - -
50A ARG* 2.5 46.3 + - - +
73A ASN* 3.9 38.5 + - - +
83A GLN* 5.9 0.9 + - - -
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Residues in contact with GLU 47 (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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43A HIS* 3.0 24.2 + - - +
44A GLN* 3.7 13.9 - - - +
46A ASP* 1.3 85.3 - - - +
48A GLU* 1.3 59.9 + - - +
50A ARG* 3.8 23.6 + - - +
51A MET* 2.8 37.7 + - - +
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Residues in contact with GLU 48 (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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41A ILE 5.2 0.2 - - - +
44A GLN* 2.4 71.6 + - - +
45A LEU* 3.9 5.2 + - - +
47A GLU* 1.3 70.7 - - - +
49A GLU* 1.3 56.5 + - - +
50A ARG 3.1 1.1 - - - -
51A MET* 2.8 15.2 - - - +
52A ARG* 2.5 44.1 + - + +
87A ASN* 5.8 3.5 - - - +
90A LYS* 6.0 2.9 - - - +
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Residues in contact with GLU 49 (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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45A LEU* 2.3 53.5 + - + +
46A ASP* 4.5 1.6 - - - +
48A GLU* 1.3 69.0 - - - +
50A ARG* 1.3 55.2 + - - +
52A ARG* 4.3 9.4 - - - +
53A MET* 2.7 65.1 + - - +
66A PHE* 3.6 28.8 - - + -
90A LYS* 6.1 3.8 - - - +
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Residues in contact with ARG 50 (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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46A ASP* 2.5 30.5 + - - +
47A GLU* 3.8 23.5 + - - +
49A GLU* 1.3 78.6 - - - +
51A MET* 1.3 52.6 + - - +
53A MET* 3.3 10.1 - - - +
54A ALA* 2.5 45.4 + - + +
63A TYR* 4.5 11.0 - - - +
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Residues in contact with MET 51 (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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47A GLU* 2.8 30.7 + - - +
48A GLU* 2.8 23.1 - - - +
50A ARG* 1.3 76.0 - - + +
52A ARG* 1.3 69.9 + - + +
54A ALA* 4.1 3.1 - - - -
55A GLU* 2.4 65.2 + - + +
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Residues in contact with ARG 52 (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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48A GLU* 2.5 32.8 + - + +
49A GLU* 4.2 9.6 - - + +
51A MET* 1.3 76.2 - - + +
53A MET* 1.3 60.4 + - - +
55A GLU* 4.6 2.7 - - - -
56A GLY* 2.8 34.8 + - - +
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Residues in contact with MET 53 (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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49A GLU* 2.7 56.2 + - - +
50A ARG* 3.3 8.1 - - - +
52A ARG* 1.3 76.2 - - - +
54A ALA* 1.3 72.1 + - - +
57A GLY 2.9 4.9 + - - -
58A VAL* 2.4 61.4 + - + +
62A ASP* 4.2 7.9 - - + +
63A TYR* 3.1 53.4 - - + -
66A PHE* 4.1 10.3 - - + -
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Residues in contact with ALA 54 (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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50A ARG* 2.5 34.4 + - + +
51A MET* 3.8 3.4 - - - +
53A MET* 1.3 78.7 - - + +
55A GLU* 1.3 63.9 + - + +
57A GLY* 3.1 12.1 + - - -
58A VAL* 4.0 6.4 - - - +
63A TYR* 4.8 7.4 - - + +
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Residues in contact with GLU 55 (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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51A MET* 2.4 66.0 + - + +
52A ARG* 4.1 3.1 - - - +
54A ALA* 1.3 65.6 - - + +
56A GLY* 1.3 55.0 + - - +
57A GLY* 2.7 15.8 + - - -
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Residues in contact with GLY 56 (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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52A ARG* 2.8 33.0 + - - +
53A MET 4.1 0.2 - - - -
55A GLU* 1.3 72.6 - - - +
57A GLY* 1.3 55.0 + - - +
58A VAL 3.2 7.3 + - - -
59A THR 4.7 1.0 + - - -
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Residues in contact with GLY 57 (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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53A MET 2.9 2.5 + - - -
54A ALA 3.4 8.7 - - - -
55A GLU 2.7 7.8 + - - -
56A GLY* 1.3 78.7 - - - +
58A VAL* 1.3 67.4 + - - +
59A THR* 2.4 22.2 + - - -
60A SER* 3.3 4.7 + - - -
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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