Contacts of the helix formed by residues 59 - 71 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 3.4 30.1 - - - +
56B GLY 4.0 2.0 + - - +
57B HIS 3.3 4.1 + - - -
58B LEU* 1.3 73.4 - - - +
60B PRO* 1.3 76.4 - - + +
61B LYS* 3.1 46.8 + - + +
62B VAL* 3.0 25.0 + - + +
63B VAL* 2.9 25.5 + - - +
314B VAL* 3.4 19.2 - - + +
318B GLU* 2.7 36.5 + - - -
404B THR* 4.4 7.2 - - + -
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Residues in contact with PRO 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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58B LEU 3.0 8.7 - - - +
59B HIS* 1.3 94.2 - - + +
61B LYS* 1.3 64.1 + - + +
63B VAL* 4.0 6.6 - - + +
64B ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 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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59B HIS* 3.1 27.5 + - + +
60B PRO* 1.3 80.1 - - + +
62B VAL* 1.3 64.6 + - - +
64B ALA* 3.4 5.7 + - + +
65B ALA* 3.1 17.8 + - - +
310B GLU* 3.3 25.5 - - + +
314B VAL* 3.8 15.0 - - + -
317B GLN* 4.4 19.0 + - - +
318B GLU* 4.7 2.5 - - - +
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Residues in contact with VAL 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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55B THR* 4.6 4.0 - - - +
58B LEU* 6.4 0.2 - - - -
59B HIS* 3.0 31.6 + - + +
61B LYS* 1.3 77.1 - - - +
63B VAL* 1.3 62.8 + - + +
65B ALA* 3.4 3.5 + - - +
66B VAL* 3.1 22.2 + - - +
271B ALA 4.4 5.6 - - - +
272B GLY 4.8 4.0 - - - +
274B PHE* 4.1 17.3 - - + -
307B ALA* 4.1 27.6 - - + +
310B GLU* 3.7 9.2 - - + -
311B VAL* 3.9 33.7 - - + +
314B VAL* 4.7 3.4 - - + -
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Residues in contact with VAL 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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70A LEU* 4.4 20.6 - - + +
71A LYS* 5.7 1.8 - - + +
58B LEU* 3.7 41.7 - - + +
59B HIS 2.9 19.9 + - - +
60B PRO* 4.0 6.7 - - + +
62B VAL* 1.3 76.2 - - + +
64B ALA* 1.3 55.3 + - - +
66B VAL* 3.2 7.7 + - - +
67B GLU* 2.7 57.5 + - + +
274B PHE* 5.3 3.8 - - + -
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Residues in contact with ALA 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 PRO 3.0 18.8 + - - +
61B LYS* 3.7 5.4 - - - +
63B VAL* 1.3 76.6 - - - +
65B ALA* 1.3 62.4 + - - +
67B GLU* 3.3 14.1 + - - +
68B ALA* 3.0 23.2 + - - +
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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 LYS 3.1 12.9 + - - +
62B VAL 3.6 8.3 - - - +
63B VAL 3.2 0.2 - - - -
64B ALA* 1.3 76.7 - - - +
66B VAL* 1.3 64.8 + - - +
68B ALA* 3.2 8.3 + - - +
69B GLN* 3.1 18.4 + - - +
306B VAL* 3.8 24.8 - - + +
310B GLU* 3.8 29.2 - - + +
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Residues in contact with VAL 66 (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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66A VAL* 6.2 0.4 - - + -
70A LEU* 3.7 31.4 - - + -
62B VAL 3.1 17.5 + - - +
63B VAL* 3.4 9.6 - - - +
65B ALA* 1.3 77.3 - - - +
67B GLU* 1.3 56.1 + - - +
69B GLN* 3.3 2.8 + - - +
70B LEU* 2.9 29.7 + - + +
274B PHE* 3.8 24.9 - - + -
303B ILE* 3.6 37.5 - - + +
306B VAL* 4.0 6.7 - - - -
307B ALA* 4.0 11.7 - - + -
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Residues in contact with GLU 67 (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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67A GLU* 5.0 11.4 - - + +
70A LEU* 4.3 19.4 - - + +
71A LYS* 3.7 27.5 + - - -
63B VAL* 2.7 40.8 + - - +
64B ALA* 3.6 13.3 - - - +
65B ALA 3.2 0.4 - - - -
66B VAL* 1.3 74.1 - - - +
68B ALA* 1.3 61.7 + - - +
70B LEU* 3.3 19.3 + - + +
71B LYS* 3.4 20.7 + - - +
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Residues in contact with ALA 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 ALA 3.0 13.3 + - - +
65B ALA* 3.2 10.3 + - - +
67B GLU* 1.3 75.0 - - - +
69B GLN* 1.3 61.8 + - - +
71B LYS* 3.1 24.2 + - - +
72B LYS* 3.7 13.4 + - + +
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Residues in contact with GLN 69 (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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28A ASP 5.1 1.0 + - - -
65B ALA 3.1 3.9 + - - +
66B VAL 3.8 2.7 - - - +
68B ALA* 1.3 73.3 - - - +
70B LEU* 1.3 58.6 + - - +
71B LYS 2.9 5.6 - - - -
72B LYS* 2.8 36.7 + - - +
73B LEU* 2.9 65.0 + - - +
85B PRO* 3.9 13.9 - - - +
302B PRO* 3.9 22.1 - - - +
303B ILE* 3.8 11.2 - - + -
306B VAL* 3.7 36.2 - - + +
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Residues in contact with LEU 70 (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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58A LEU* 3.5 27.0 - - + +
63A VAL* 3.9 21.4 - - + +
66A VAL* 3.6 21.3 - - + -
67A GLU* 3.4 34.5 - - + +
70A LEU* 4.2 12.3 - - + -
274A PHE* 3.8 31.6 - - + -
66B VAL* 2.9 18.6 + - + +
67B GLU* 3.5 9.6 - - + +
69B GLN* 1.3 76.8 - - - +
71B LYS* 1.3 61.3 + - - +
72B LYS 3.3 0.2 - - - -
73B LEU 4.8 0.7 - - - -
74B SER* 4.8 0.2 - - - -
303B ILE* 3.7 16.8 - - + +
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Residues in contact with LYS 71 (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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29A ARG* 5.3 1.2 - - - +
30A ALA 5.2 0.7 - - - +
58A LEU* 3.9 6.9 - - - +
63A VAL* 5.3 4.1 - - + +
67A GLU* 3.0 30.8 + - - +
67B GLU* 3.5 15.0 - - - +
68B ALA* 3.1 14.0 + - - +
69B GLN 2.9 1.0 - - - -
70B LEU* 1.3 80.2 - - - +
72B LYS* 1.3 63.1 + - + +
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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