Contacts of the helix formed by residues 59 - 70 (chain A) in PDB entry 1SZU
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A THR* 3.5 32.5 - - - +
56A GLY 3.9 2.0 + - - -
57A HIS 3.4 3.9 + - - -
58A LEU* 1.3 72.4 - - - +
60A PRO* 1.3 79.6 - - + +
61A LYS* 2.9 54.1 + - + +
62A VAL* 3.1 25.6 + - + +
63A VAL* 2.9 23.3 + - - +
272A GLY 5.7 1.0 + - - -
314A VAL* 3.6 18.3 - - + +
318A GLU* 2.8 31.5 + - - -
404A THR* 4.5 5.2 - - + -
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Residues in contact with PRO 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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58A LEU 3.2 6.9 - - - +
59A HIS* 1.3 99.4 - - + +
61A LYS* 1.3 59.8 + - + +
63A VAL* 3.9 5.4 - - + +
64A ALA* 2.9 31.5 + - - +
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Residues in contact with LYS 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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59A HIS* 2.9 30.5 + - + +
60A PRO* 1.3 76.3 - - + +
62A VAL* 1.3 62.1 + - - +
64A ALA* 3.7 6.5 - - + +
65A ALA* 3.1 18.0 + - - +
310A GLU* 3.2 32.5 - - + +
314A VAL* 4.0 9.6 - - + -
317A GLN* 4.2 20.2 - - - +
318A GLU* 5.0 2.2 - - - +
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Residues in contact with VAL 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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55A THR* 4.7 3.4 - - - +
59A HIS* 3.1 30.9 + - + +
61A LYS* 1.3 77.6 - - - +
63A VAL* 1.3 58.6 + - + +
65A ALA* 3.2 4.2 + - - +
66A VAL* 2.9 28.1 + - - +
271A ALA 4.6 3.8 - - - +
272A GLY 4.9 4.7 - - - +
274A PHE* 4.0 26.7 - - + -
307A ALA* 4.0 19.2 - - + +
310A GLU* 3.8 20.0 - - + -
311A VAL* 4.0 25.1 - - + +
314A VAL* 4.8 2.2 - - + -
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Residues in contact with VAL 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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58A LEU* 3.6 40.4 - - + +
59A HIS 2.9 20.2 + - - +
60A PRO* 3.9 5.8 - - + +
62A VAL* 1.3 74.4 - - + +
64A ALA* 1.3 62.0 + - - +
66A VAL* 3.3 7.3 + - - +
67A GLU* 2.8 56.0 + - - +
274A PHE* 5.5 1.6 - - + -
70B LEU* 3.9 24.9 - - + +
71B LYS* 5.3 3.8 - - + +
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Residues in contact with ALA 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 PRO 2.9 18.6 + - - +
61A LYS* 3.7 7.2 - - + +
63A VAL* 1.3 76.1 - - - +
65A ALA* 1.3 62.6 + - - +
67A GLU* 3.4 15.1 + - - +
68A ALA* 3.1 23.2 + - - +
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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 LYS 3.1 14.5 + - - +
62A VAL 3.5 8.1 - - - +
64A ALA* 1.3 77.4 - - - +
66A VAL* 1.3 62.7 + - - +
68A ALA* 3.2 8.0 + - - +
69A GLN* 3.1 22.5 + - - +
306A VAL* 3.9 19.6 - - + +
310A GLU* 4.0 26.2 - - + +
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Residues in contact with VAL 66 (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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62A VAL 2.9 20.7 + - - +
63A VAL* 3.6 6.7 - - - +
65A ALA* 1.3 77.1 - - - +
67A GLU* 1.3 62.6 + - - +
69A GLN* 3.3 3.6 + - - +
70A LEU* 3.0 28.2 + - + +
274A PHE* 4.0 15.3 - - + -
303A ILE* 3.7 30.8 - - + +
306A VAL* 4.0 7.6 - - + +
307A ALA* 3.8 26.7 - - + -
66B VAL* 6.2 0.7 - - + -
70B LEU* 3.6 28.3 - - + -
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Residues in contact with GLU 67 (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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63A VAL* 2.8 42.2 + - - +
64A ALA* 3.7 13.4 - - - +
65A ALA 3.3 0.2 - - - -
66A VAL* 1.3 72.5 - - - +
68A ALA* 1.3 63.4 + - - +
70A LEU* 3.4 22.0 + - + +
71A LYS* 3.6 17.6 - - - +
67B GLU* 5.0 10.7 - - + +
70B LEU* 3.4 20.4 - - + +
71B LYS* 3.0 34.1 + - - +
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Residues in contact with ALA 68 (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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64A ALA 3.1 13.1 + - - +
65A ALA* 3.2 10.5 + - - +
67A GLU* 1.3 75.4 - - - +
69A GLN* 1.3 63.6 + - - +
71A LYS* 3.0 25.6 + - - +
72A LYS* 3.9 15.7 + - - +
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Residues in contact with GLN 69 (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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65A ALA 3.1 12.3 + - - +
66A VAL 3.7 7.6 - - - +
68A ALA* 1.3 76.8 - - - +
70A LEU* 1.3 57.7 + - - +
71A LYS 3.0 0.2 - - - -
72A LYS* 2.9 26.9 + - - +
73A LEU* 3.1 43.1 + - - +
85A PRO* 4.7 0.2 - - - -
302A PRO* 3.9 6.5 - - - +
303A ILE* 3.9 20.0 - - + +
306A VAL* 3.7 29.9 - - + +
1030A EDO 2.7 49.3 + - - -
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Residues in contact with LEU 70 (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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66A VAL* 3.0 19.5 + - + +
67A GLU* 3.5 11.9 - - - +
68A ALA 3.2 0.4 - - - -
69A GLN* 1.3 75.5 - - - +
71A LYS* 1.3 60.1 + - - +
72A LYS 3.3 0.2 - - - -
73A LEU 4.8 1.3 - - - -
303A ILE* 4.1 16.4 - - + +
58B LEU* 3.3 33.8 - - + +
63B VAL* 4.4 15.2 - - + +
66B VAL* 3.7 22.9 - - + -
67B GLU* 4.3 25.1 - - + +
70B LEU* 4.2 18.8 - - + -
274B PHE* 3.8 35.0 - - + -
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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