Contacts of the helix formed by residues 49 - 65 (chain A) in PDB entry 2AG1
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 HIS 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 4.0 - - - +
47A THR* 2.7 20.2 + - - -
48A ARG* 1.3 80.2 - - - +
50A GLU* 1.3 67.3 + - - +
51A ALA* 2.9 40.6 + - + +
52A ALA* 3.2 9.1 + - + +
53A ALA 3.1 7.8 + - - -
80A ASN* 3.8 29.1 + - + -
453A TYR 5.1 6.7 - - - -
454A SER* 5.6 5.2 - - - +
457A GLU* 3.4 9.1 + - - +
49B HIS* 4.2 20.7 + + - -
452B GLY 5.6 0.9 - - - +
453B TYR* 3.5 44.1 + + - -
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Residues in contact with GLU 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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25A LEU* 3.1 28.3 - - + +
49A HIS* 1.3 70.3 + - - +
51A ALA* 1.3 66.2 + - - +
53A ALA* 3.0 8.5 + - - +
54A GLY* 2.8 22.3 + - - -
72A VAL* 3.5 22.2 - - + +
73A THR* 4.7 6.2 - - - +
77A GLY* 3.4 40.7 - - - +
80A ASN* 3.1 25.9 + - + -
81A ALA* 4.2 3.4 - - - +
84A PRO* 4.6 0.7 - - - +
453B TYR* 2.7 28.6 + - - -
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Residues in contact with ALA 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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49A HIS* 2.9 24.0 + - + +
50A GLU* 1.3 78.4 - - - +
52A ALA* 1.3 56.5 + - - +
54A GLY 3.2 0.3 + - - -
55A HIS* 2.9 43.1 + - + +
80A ASN 3.4 19.8 + - - +
83A THR* 5.4 3.4 - - - -
84A PRO* 3.2 14.9 - - + +
454A SER* 5.6 3.1 - - - +
49B HIS* 5.7 4.0 - - - +
80B ASN* 5.8 2.5 - - - +
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Residues in contact with ALA 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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47A THR* 4.2 4.7 - - + -
49A HIS* 3.2 12.6 + - + +
51A ALA* 1.3 78.9 - - - +
53A ALA* 1.3 55.1 + - - +
55A HIS* 3.3 3.7 + - - -
56A ALA* 2.8 30.1 + - - +
426A GLY* 3.6 18.5 - - - +
429A LEU* 6.2 0.2 - - + -
454A SER* 4.5 9.9 + - - +
457A GLU* 3.4 43.1 - - + +
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Residues in contact with ALA 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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23A PHE* 3.4 13.5 - - - +
24A GLY* 3.9 30.7 - - - +
25A LEU 4.7 0.2 - - - +
47A THR* 3.3 25.9 + - + +
49A HIS 3.1 6.1 + - - +
50A GLU* 3.0 14.4 + - + +
52A ALA* 1.3 74.3 - - - +
54A GLY* 1.3 57.7 + - - +
56A ALA* 3.2 6.5 + - - +
57A ALA* 3.0 24.6 + - - +
72A VAL* 5.2 4.3 - - + -
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Residues in contact with GLY 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 GLU 2.8 12.8 + - - -
51A ALA 3.6 2.9 - - - -
53A ALA* 1.3 77.1 - - - +
55A HIS* 1.3 60.4 + - - +
57A ALA* 3.2 6.4 + - - +
58A GLU* 3.1 23.4 + - - +
70A ALA* 4.2 7.4 - - - +
72A VAL* 5.9 0.8 - - - +
81A ALA* 5.7 1.6 - - - -
84A PRO* 3.6 20.7 - - - +
97A PHE* 4.0 16.2 - - - -
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Residues in contact with HIS 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 ALA* 2.9 31.6 + - + +
52A ALA* 3.8 3.6 - - - +
54A GLY* 1.3 73.0 - - - +
56A ALA* 1.3 59.6 + - - +
58A GLU* 2.6 28.1 + - - +
59A GLY 2.8 23.6 + - - -
83A THR* 3.9 9.2 - - - +
84A PRO* 3.4 34.2 - - + +
87A ASN* 4.5 1.6 - - + -
422A GLY 5.0 2.0 - - - -
423A VAL* 3.3 48.3 - - + +
426A GLY* 3.7 6.7 - - - -
427A THR* 3.3 27.8 - - - +
454A SER* 5.7 2.9 - - - -
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Residues in contact with ALA 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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23A PHE* 3.5 24.7 - - + -
47A THR* 5.2 0.7 - - + -
52A ALA 2.8 14.9 + - - +
53A ALA* 3.4 11.2 - - - +
54A GLY 3.2 0.2 - - - -
55A HIS* 1.3 74.0 - - - +
57A ALA* 1.3 56.0 + - - +
59A GLY 3.0 1.0 + - - -
60A TYR* 2.7 33.6 + - - +
426A GLY 3.1 17.4 + - - +
429A LEU* 4.1 9.6 - - + -
430A GLY* 3.2 15.2 - - - +
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Residues in contact with ALA 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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23A PHE* 3.9 12.9 - - + -
53A ALA 3.0 9.3 + - - +
54A GLY 3.4 9.6 - - - +
56A ALA* 1.3 75.0 - - - +
58A GLU* 1.3 56.5 + - - +
60A TYR* 3.4 2.8 + - - +
61A ALA* 2.9 29.5 + - - +
68A GLY* 3.6 4.9 - - - -
69A VAL 4.0 15.9 - - - +
70A ALA* 3.9 18.4 - - + -
95A VAL* 3.7 25.6 - - + -
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Residues in contact with GLU 58 (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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54A GLY 3.1 10.2 + - - +
55A HIS* 2.6 42.1 + - - +
57A ALA* 1.3 75.0 - - - +
59A GLY* 1.3 53.4 + - - +
61A ALA* 3.0 3.3 + - - +
62A ARG* 2.6 50.1 + - - +
84A PRO* 3.4 21.0 - - + +
87A ASN* 3.1 20.6 - - - +
88A ALA* 3.3 23.0 + - + -
91A ASP* 4.5 1.2 - - - +
93A THR* 4.1 11.8 - - - +
95A VAL* 3.8 20.4 - - + +
97A PHE* 5.1 0.9 - - + -
427A THR* 5.1 4.0 - - - +
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Residues in contact with GLY 59 (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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55A HIS 2.8 13.7 + - - -
56A ALA 3.5 1.8 - - - -
58A GLU* 1.3 73.5 - - - +
60A TYR* 1.3 56.4 + - - +
62A ARG* 4.1 0.2 - - - +
63A ALA* 2.9 36.9 + - - +
413A LEU* 4.2 4.7 - - - -
427A THR* 3.4 35.0 - - - -
431A ALA 3.6 7.6 - - - -
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Residues in contact with TYR 60 (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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20A GLU* 4.4 8.0 + - - +
21A HIS* 2.9 51.7 + + + +
23A PHE* 3.5 27.8 - + + -
56A ALA 2.7 19.9 + - - +
57A ALA 3.5 3.8 - - - +
59A GLY* 1.3 72.3 - - - +
61A ALA* 1.3 56.7 + - - +
64A GLY* 3.0 27.5 + - - -
66A LYS* 3.5 34.5 - - + +
67A LEU 3.5 25.4 - - - -
68A GLY* 4.1 6.5 - - - -
69A VAL 5.8 0.2 - - - -
430A GLY 3.5 10.0 - - - +
433A VAL* 4.0 2.2 - - + -
434A ALA* 3.7 34.9 - - + +
437A GLU* 3.9 1.7 + - - -
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Residues in contact with ALA 61 (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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57A ALA 2.9 14.7 + - - +
58A GLU* 3.5 7.0 - - - +
60A TYR* 1.3 76.1 - - - +
62A ARG* 1.3 56.4 + - - +
65A ALA* 2.7 34.5 + - - -
66A LYS 3.1 27.0 + - - +
67A LEU 4.6 0.2 - - - -
68A GLY 3.6 4.7 - - - +
93A THR* 4.4 3.8 - - - +
94A PRO* 3.6 30.7 - - + +
217A ARG* 5.3 2.6 + - - -
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Residues in contact with ARG 62 (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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58A GLU* 2.6 33.0 + - - +
59A GLY 4.7 0.2 - - - +
61A ALA* 1.3 72.5 - - - +
63A ALA* 1.3 60.6 + - - +
65A ALA* 4.2 4.0 + - - +
87A ASN* 4.6 8.1 + - - -
91A ASP* 4.0 15.8 + - - -
93A THR* 3.9 25.1 - - - -
216A SER* 4.7 8.0 + - - -
217A ARG* 3.8 18.6 + - - +
240A GLU* 2.7 41.4 + - - +
413A LEU* 3.5 32.7 - - + +
414A CYS 2.8 39.6 + - - +
423A VAL* 5.3 3.0 - - - +
427A THR* 3.9 21.8 + - - +
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Residues in contact with ALA 63 (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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59A GLY 2.9 17.6 + - - +
60A TYR 4.6 0.2 - - - +
62A ARG* 1.3 77.4 - - - +
64A GLY* 1.3 58.9 + - - +
65A ALA 3.5 0.7 - - - -
388A THR* 4.4 10.3 - - + +
410A GLY 5.4 1.0 - - - +
411A GLY* 6.0 2.9 - - - -
413A LEU* 4.1 10.3 - - + -
431A ALA* 3.7 25.6 - - + +
434A ALA* 4.7 2.7 - - + -
435A ASP* 4.2 12.1 - - - +
440A ARG* 3.5 24.1 + - - +
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Residues in contact with GLY 64 (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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60A TYR 3.0 16.3 + - - -
63A ALA* 1.3 77.0 - - - +
65A ALA* 1.3 73.4 + - - +
66A LYS* 3.3 21.5 + - - +
434A ALA* 4.1 14.0 - - - +
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Residues in contact with ALA 65 (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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61A ALA 2.7 18.2 + - - -
62A ARG 4.2 4.3 + - - +
63A ALA 3.5 2.8 - - - -
64A GLY* 1.3 75.5 - - - +
66A LYS* 1.3 55.9 + - - +
94A PRO* 6.1 0.7 - - - -
216A SER 4.0 13.9 - - - +
217A ARG* 3.9 28.6 - - - +
219A ALA* 4.5 13.0 - - + -
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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