Contacts of the helix formed by residues 49 - 65 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 4.2 20.1 + + - -
452A GLY 5.8 0.4 - - - +
453A TYR* 3.5 46.1 + + - -
25B LEU* 3.5 2.4 - - - +
47B THR* 2.9 17.7 + - - -
48B ARG* 1.3 80.9 - - - +
50B GLU* 1.3 69.6 + - - +
51B ALA* 2.9 40.5 + - + +
52B ALA* 3.0 11.3 + - + +
53B ALA 3.0 8.3 + - - -
80B ASN* 3.8 28.3 + - + -
453B TYR 5.1 6.5 - - - -
454B SER* 5.6 4.9 - - - +
457B GLU* 3.3 9.3 + - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A TYR* 2.7 29.2 + - - -
25B LEU* 3.2 27.7 - - + +
49B HIS* 1.3 69.7 + - - +
51B ALA* 1.3 55.7 + - - +
53B ALA* 3.2 8.5 + - - +
54B GLY* 2.8 31.9 + - - -
72B VAL* 3.5 27.6 - - + +
73B THR* 4.6 6.8 + - - +
77B GLY* 3.5 34.9 - - - +
80B ASN* 3.2 26.0 + - + -
81B ALA* 4.3 3.7 - - - +
84B PRO* 4.5 1.2 - - - +
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Residues in contact with ALA 51 (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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49A HIS* 5.6 4.3 - - - +
80A ASN* 5.9 2.0 - - - +
49B HIS* 2.9 26.4 + - + +
50B GLU* 1.3 76.4 - - - +
52B ALA* 1.3 57.4 + - - +
54B GLY 3.1 2.1 + - - -
55B HIS* 2.9 42.3 + - + +
80B ASN 3.4 16.7 + - - +
83B THR* 5.5 3.4 - - - -
84B PRO* 3.2 15.0 - - + +
454B SER* 5.7 3.4 - - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 4.2 4.9 - - + +
49B HIS* 3.0 11.6 + - + +
51B ALA* 1.3 76.6 - - - +
53B ALA* 1.3 57.7 + - - +
55B HIS* 3.4 3.4 + - - -
56B ALA* 2.9 30.3 + - - +
426B GLY* 3.6 18.3 - - - -
454B SER* 4.5 11.0 + - - +
457B GLU* 3.3 44.2 - - + +
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Residues in contact with ALA 53 (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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23B PHE* 3.4 16.3 - - - +
24B GLY* 3.8 31.9 - - - +
47B THR* 3.3 25.6 + - + +
49B HIS 3.0 6.9 + - - +
50B GLU* 3.2 13.2 + - + +
52B ALA* 1.3 75.3 - - - +
54B GLY* 1.3 62.2 + - - +
56B ALA* 3.2 3.2 + - - -
57B ALA* 3.1 19.1 + - - +
70B ALA* 5.7 0.2 - - + -
72B VAL* 5.2 3.6 - - + -
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Residues in contact with GLY 54 (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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50B GLU 2.8 17.6 + - - -
51B ALA 3.1 2.9 + - - -
53B ALA* 1.3 72.4 - - - +
55B HIS* 1.3 62.1 + - - +
57B ALA* 3.2 6.1 + - - +
58B GLU* 3.1 23.0 + - - +
70B ALA* 4.3 7.4 - - - +
81B ALA* 5.7 1.1 - - - -
84B PRO* 3.6 19.3 - - - +
97B PHE* 3.9 16.7 - - - -
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Residues in contact with HIS 55 (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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51B ALA* 2.9 32.2 + - + +
52B ALA* 3.9 3.6 - - - +
54B GLY* 1.3 73.8 - - - +
56B ALA* 1.3 61.2 + - - +
58B GLU* 2.6 28.6 + - - +
59B GLY 2.8 22.9 + - - -
83B THR* 4.0 9.2 - - + +
84B PRO* 3.4 33.3 - - + +
87B ASN* 4.5 1.8 - - + -
422B GLY 5.0 2.5 - - - -
423B VAL* 3.4 49.7 - - + +
426B GLY* 3.6 6.7 - - - -
427B THR* 3.3 28.7 - - - +
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Residues in contact with ALA 56 (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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23B PHE* 3.5 25.4 - - + -
47B THR* 5.2 0.9 - - + -
52B ALA 2.9 18.4 + - - +
53B ALA* 3.4 8.5 - - - +
55B HIS* 1.3 75.5 - - - +
57B ALA* 1.3 56.7 + - - +
59B GLY 2.9 1.2 + - - -
60B TYR* 2.7 34.1 + - - +
426B GLY 3.0 16.3 + - - +
429B LEU* 4.2 8.7 - - + -
430B GLY* 3.2 15.6 - - - +
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Residues in contact with ALA 57 (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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23B PHE* 3.8 12.7 - - + -
53B ALA 3.1 12.2 + - - +
54B GLY 3.2 10.0 + - - +
56B ALA* 1.3 76.5 - - - +
58B GLU* 1.3 60.9 + - - +
60B TYR* 3.7 0.5 - - - +
61B ALA* 3.0 23.9 + - - +
68B GLY* 3.6 6.4 - - - -
69B VAL 4.0 16.2 - - - +
70B ALA* 3.9 13.5 - - + -
95B VAL* 3.6 25.4 - - + -
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Residues in contact with GLU 58 (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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54B GLY 3.1 10.2 + - - +
55B HIS* 2.6 44.2 + - - +
56B ALA 3.2 0.2 - - - -
57B ALA* 1.3 75.3 - - - +
59B GLY* 1.3 52.1 + - - +
61B ALA* 3.0 2.5 + - - +
62B ARG* 2.7 49.4 + - - +
84B PRO* 3.5 17.9 - - + +
87B ASN* 3.0 21.0 - - - +
88B ALA* 3.3 22.6 + - + -
91B ASP* 4.6 1.2 - - - +
93B THR* 4.1 10.9 - - - +
95B VAL* 3.8 19.9 - - + +
97B PHE* 5.1 0.9 - - + -
427B THR* 5.1 4.5 - - - +
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B HIS 2.8 14.4 + - - -
56B ALA 2.9 1.9 + - - -
58B GLU* 1.3 71.7 - - - +
60B TYR* 1.3 56.8 + - - +
62B ARG* 4.6 0.2 - - - -
63B ALA* 2.9 35.9 + - - +
413B LEU* 4.0 5.0 - - - +
427B THR* 3.3 34.5 - - - -
431B ALA* 3.6 7.3 - - - +
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Residues in contact with TYR 60 (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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20B GLU* 4.4 8.1 + - - +
21B HIS* 2.9 51.6 + + + +
23B PHE* 3.5 28.9 - + + -
56B ALA 2.7 19.7 + - - +
57B ALA 3.7 3.1 - - - +
59B GLY* 1.3 72.4 - - - +
61B ALA* 1.3 57.0 + - - +
64B GLY* 3.0 26.7 + - - -
66B LYS* 3.5 39.2 - - + +
67B LEU 3.6 21.1 - - - -
68B GLY* 4.2 6.1 - - - -
69B VAL 5.4 0.2 - - - -
430B GLY 3.5 10.9 - - - +
433B VAL* 4.0 6.7 - - + -
434B ALA* 3.7 29.0 - - + +
437B GLU* 3.9 1.2 + - - -
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Residues in contact with ALA 61 (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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57B ALA 3.0 16.8 + - - +
58B GLU* 3.0 5.6 + - - +
60B TYR* 1.3 75.6 - - - +
62B ARG* 1.3 58.3 + - - +
65B ALA* 2.8 34.3 + - - -
66B LYS 3.1 26.1 + - - +
68B GLY 3.7 4.5 - - - +
93B THR* 4.4 3.8 - - - +
94B PRO* 3.6 31.2 - - + +
217B ARG* 5.3 2.8 + - - -
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Residues in contact with ARG 62 (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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58B GLU* 2.7 32.5 + - - +
59B GLY* 4.8 0.7 - - - +
61B ALA* 1.3 72.3 - - - +
63B ALA* 1.3 60.6 + - - +
65B ALA* 4.1 4.5 + - - +
87B ASN* 4.5 8.1 + - - -
91B ASP* 3.9 17.7 + - - -
93B THR* 4.0 23.6 - - - -
216B SER* 4.7 7.1 + - - -
217B ARG* 3.8 19.0 + - - +
240B GLU* 2.7 43.7 + - - +
413B LEU* 3.4 30.7 - - + +
414B CYS 2.8 39.4 + - - +
423B VAL* 5.5 2.8 - - - +
427B THR* 4.0 19.4 + - - +
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Residues in contact with ALA 63 (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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59B GLY 2.9 18.7 + - - +
60B TYR 4.6 0.4 - - - +
62B ARG* 1.3 77.0 - - - +
64B GLY* 1.3 60.1 + - - +
65B ALA 3.5 0.2 - - - -
388B THR* 4.5 9.6 - - + +
411B GLY* 6.0 2.9 - - - -
413B LEU* 4.1 10.3 - - + -
431B ALA* 3.8 25.1 - - + +
434B ALA* 4.6 2.9 - - + +
435B ASP* 4.4 11.9 - - - +
440B ARG* 3.5 23.1 + - - +
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Residues in contact with GLY 64 (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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60B TYR 3.0 16.9 + - - -
63B ALA* 1.3 76.8 - - - +
65B ALA* 1.3 72.4 + - - +
66B LYS* 3.2 22.2 + - - +
434B ALA* 4.1 12.7 - - - +
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Residues in contact with ALA 65 (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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61B ALA 2.8 14.3 + - - -
62B ARG 4.1 4.1 + - - +
63B ALA 3.5 2.8 - - - -
64B GLY* 1.3 79.4 - - - +
66B LYS* 1.3 56.1 + - - +
94B PRO* 6.2 0.7 - - - -
216B SER 4.0 13.7 - - - +
217B ARG* 3.9 28.5 - - - +
219B ALA* 4.5 13.2 - - + -
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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