Contacts of the helix formed by residues 48 - 68 (chain B) in PDB entry 1ATH
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 VAL 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 1.3 61.1 + - - +
50B GLU* 3.1 10.6 - - - +
51B LEU* 2.8 32.6 + - - +
52B SER* 2.9 13.0 + - - +
122B PHE* 4.6 18.5 - - + +
125B LYS* 3.8 30.5 - - + -
126B LEU* 3.7 37.7 - - + +
129B ARG* 5.5 7.6 - - - -
417B LEU* 4.3 17.0 - - + -
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Residues in contact with TRP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 1.3 77.9 - - - +
50B GLU* 1.3 71.6 + - + +
52B SER* 3.0 10.0 + - - -
53B LYS* 2.9 52.1 + - + +
305B GLN* 5.0 12.3 - - - -
416B PRO 5.0 7.6 + - - -
417B LEU* 4.7 11.0 - - + +
418B ASN* 2.9 29.0 + - - +
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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
----------------------------------------------------------
48B VAL 4.8 7.4 - - - +
49B TRP* 1.3 88.4 - - + +
51B LEU* 1.3 60.4 + - - +
53B LYS* 3.4 7.7 + - - +
54B ALA* 3.1 21.8 + - - +
110B THR* 4.7 4.7 - - - +
111B ILE* 3.8 44.7 - - + +
122B PHE* 6.0 0.2 - - - -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 2.8 16.0 + - - +
50B GLU* 1.3 77.0 - - - +
52B SER* 1.3 56.6 + - - +
54B ALA* 3.1 3.9 + - + +
55B ASN* 2.9 44.9 + - - +
108B PHE* 3.7 24.9 - - + -
111B ILE* 3.6 30.2 - - + +
119B ILE* 5.0 2.9 - - + -
122B PHE* 3.6 15.7 - - + +
123B PHE* 3.5 44.9 - - + +
126B LEU* 3.9 15.5 - - + -
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 2.9 13.6 + - - +
49B TRP* 3.2 12.6 - - - -
51B LEU* 1.3 75.6 - - - +
53B LYS* 1.3 55.2 + - - +
55B ASN* 3.2 8.2 + - - +
56B SER* 2.8 35.5 + - - -
126B LEU* 3.6 20.6 - - - +
417B LEU* 3.3 29.2 + - - +
418B ASN* 3.9 10.5 - - - -
419B THR* 5.2 5.6 - - - +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 2.9 47.6 + - + +
50B GLU* 3.4 11.7 - - - +
52B SER* 1.3 72.7 - - - +
54B ALA* 1.3 66.3 + - - +
56B SER* 3.2 8.0 + - - -
57B ARG* 2.8 68.7 + - - +
110B THR* 5.9 4.9 - - + -
301B PRO* 5.0 7.5 - - + +
302B GLU* 3.3 15.5 + - - +
305B GLN* 6.2 2.2 - - - +
418B ASN* 4.3 6.7 - - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 3.1 10.4 + - - +
51B LEU* 3.3 11.2 - - + +
53B LYS* 1.3 75.2 - - - +
55B ASN* 1.3 65.6 + - - +
57B ARG* 3.0 19.4 + - - +
58B PHE* 3.0 11.1 + - - +
106B PHE 4.5 2.9 - - - +
107B LYS* 3.1 41.8 - - - +
108B PHE* 4.7 0.4 - - + -
110B THR* 4.6 7.1 - - - +
111B ILE* 4.1 15.0 - - + -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.9 24.8 + - - +
52B SER* 3.3 12.2 - - - +
54B ALA* 1.3 77.2 - - - +
56B SER* 1.3 57.2 + - - +
58B PHE* 3.1 9.9 + - - +
59B ALA* 2.9 26.7 + - - +
80B PRO* 5.2 2.0 - - - +
81B LEU* 4.9 8.2 - - + +
84B SER* 3.3 33.4 + - - +
106B PHE 4.7 3.6 + - - -
108B PHE* 4.2 12.1 - - - -
123B PHE* 3.7 25.2 - - - -
126B LEU* 5.1 3.5 - - - +
419B THR* 5.9 4.4 - - + +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER 2.8 19.5 + - - -
53B LYS* 3.5 7.9 - - - -
55B ASN* 1.3 72.6 - - - +
57B ARG* 1.3 57.8 + - - +
59B ALA* 2.9 29.3 + - - +
60B THR* 3.1 13.7 + - - +
301B PRO* 3.8 16.6 - - - -
413B ARG* 6.1 0.7 - - - -
418B ASN* 3.5 26.0 + - - -
419B THR* 5.2 0.5 - - - -
420B ILE* 4.5 18.8 + - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 2.8 54.9 + - - +
54B ALA* 3.3 9.4 - - - +
56B SER* 1.3 75.2 - - - +
58B PHE* 1.3 59.3 + - - +
60B THR* 3.1 7.4 + - - -
61B THR* 2.6 35.3 + - - +
107B LYS* 4.1 22.0 - - + +
110B THR* 4.8 16.9 - - - +
301B PRO* 3.6 21.8 - - + +
302B GLU* 2.8 30.1 + - - -
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 3.0 11.9 + - - +
55B ASN* 3.1 9.4 + - - +
57B ARG* 1.3 76.4 - - - +
59B ALA* 1.3 55.9 + - - +
61B THR* 3.1 3.7 + - - -
62B PHE* 2.6 65.7 + + + +
80B PRO* 5.0 5.6 - - + -
83B ILE* 4.3 14.8 - - + -
84B SER* 3.4 20.4 - - - +
105B VAL* 3.0 28.5 - - + +
106B PHE* 3.4 40.8 - + - -
107B LYS* 3.9 8.0 - - + +
335B LEU* 3.6 11.2 - - + -
338B MET* 3.8 25.1 - - + -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN 2.9 11.9 + - - +
56B SER* 2.9 15.9 + - - +
58B PHE* 1.3 76.5 - - - +
60B THR* 1.3 58.7 + - - +
62B PHE* 3.7 3.7 - - - +
63B TYR* 2.9 28.4 + - - +
78B LEU* 5.2 0.2 - - - +
80B PRO* 3.6 36.3 - - + +
420B ILE* 4.5 9.4 - - + -
423B MET* 3.7 17.5 - - + +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 3.1 10.0 + - - +
57B ARG* 3.1 10.2 + - - +
59B ALA* 1.3 79.2 - - + +
61B THR* 1.3 65.5 + - - +
63B TYR* 2.9 23.9 + - - +
64B GLN* 2.9 21.1 + - - +
299B LEU* 3.7 43.7 + - + +
300B THR 4.3 0.9 - - - +
301B PRO* 3.6 26.9 - - + +
304B LEU* 5.2 2.7 - - + -
420B ILE* 5.0 7.6 - - + -
423B MET* 4.3 10.1 - - + -
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Residues in contact with THR 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 ARG* 2.6 29.6 + - - +
58B PHE* 3.1 4.8 + - - -
60B THR* 1.3 80.9 + - - +
62B PHE* 1.3 59.4 + - - +
64B GLN* 3.7 14.0 + - - +
65B HIS* 2.8 44.5 + - + +
107B LYS* 4.6 9.1 - - - +
338B MET* 3.7 23.1 - - + -
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Residues in contact with PHE 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 PHE* 2.6 53.4 + + + +
59B ALA* 3.7 4.9 - - - +
61B THR* 1.3 70.8 - - - +
63B TYR* 1.3 65.1 + - - +
65B HIS* 3.1 6.2 + - - +
66B LEU* 2.9 44.6 + - + +
78B LEU* 3.6 24.5 - - + -
80B PRO* 6.2 0.4 - - + -
83B ILE* 4.3 4.3 - - + -
329B PHE* 3.8 16.8 - + - -
331B LEU* 3.6 28.7 - - + -
334B GLN* 3.9 24.7 - - + -
335B LEU* 3.6 22.2 - - + -
338B MET* 4.1 10.0 - - - -
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Residues in contact with TYR 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 ALA 2.9 14.3 + - - +
60B THR* 2.9 12.6 + - - +
62B PHE* 1.3 77.8 - - - +
64B GLN* 1.3 59.9 - - + +
66B LEU* 3.1 7.1 + - + +
67B ALA* 2.6 49.2 + - + +
76B ILE* 3.4 26.9 - - + -
78B LEU* 4.4 10.3 - - + -
296B GLU* 2.8 47.3 + - + +
299B LEU* 5.2 9.4 - - + -
409B LEU* 4.6 10.2 - - + +
423B MET* 3.6 28.5 - - + -
424B GLY* 4.4 15.5 - - - -
425B ARG* 3.3 20.4 + - - +
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Residues in contact with GLN 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 THR 2.9 19.1 + - - +
61B THR* 3.9 15.8 + - - +
63B TYR* 1.3 78.0 - - + +
65B HIS* 1.3 64.0 + - + +
67B ALA* 3.0 8.2 + - - +
68B ASP* 2.9 32.5 + - - +
296B GLU 2.9 31.5 + - - +
297B LYS* 3.6 26.0 + - + +
298B GLU 4.5 0.2 - - - -
299B LEU* 3.3 23.6 + - + +
300B THR* 5.7 1.2 - - - +
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Residues in contact with HIS 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 THR* 2.8 35.0 + - + +
62B PHE* 3.1 9.2 + - - +
64B GLN* 1.3 79.7 - - + +
66B LEU* 1.3 57.6 + - - +
68B ASP* 3.8 4.7 + - - +
69B SER* 3.2 21.1 + - - -
334B GLN* 3.9 20.5 - - + +
337B ASP* 3.9 29.0 + - - -
338B MET* 3.4 30.9 - - + +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 2.9 37.0 + - + +
63B TYR* 3.5 6.3 - - - +
65B HIS* 1.3 72.8 - - - +
67B ALA* 1.3 63.3 + - - +
69B SER* 2.6 18.0 + - - +
70B LYS* 3.4 34.5 + - + +
76B ILE* 4.2 21.3 - - + -
78B LEU* 5.2 7.0 - - + -
329B PHE* 4.0 37.7 - - + -
330B SER 5.7 0.4 - - - +
334B GLN* 3.6 24.9 - - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 2.6 40.1 + - + +
64B GLN* 3.4 6.3 - - - +
66B LEU* 1.3 72.7 - - - +
68B ASP* 1.3 57.9 + - - +
70B LYS* 3.0 28.1 + - - +
76B ILE* 4.0 5.8 - - + -
296B GLU* 4.0 0.4 - - - +
297B LYS* 3.5 18.6 - - - +
425B ARG* 3.8 22.2 + - - +
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Residues in contact with ASP 68 (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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64B GLN* 2.9 17.3 + - - +
65B HIS* 4.2 4.9 - - - +
67B ALA* 1.3 74.2 - - - +
69B SER* 1.3 60.3 + - - +
70B LYS 3.2 5.4 + - - +
297B LYS* 3.3 32.5 + - - +
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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
------------------------------------------------------------
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