Contacts of the helix formed by residues 62 - 75 (chain A) in PDB entry 4DHZ
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 SER 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU 4.3 0.7 + - - -
57A TYR* 3.3 21.0 - - - +
58A ASP* 3.1 26.4 + - - +
61A THR* 1.3 83.8 + - - +
63A ALA* 1.3 63.7 + - - +
64A ALA 3.5 2.2 - - - -
65A PHE* 3.8 11.1 + - - -
66A LEU* 3.3 19.1 + - - +
560E ASN* 3.8 20.3 + - - -
562E GLN* 4.0 2.6 + - - -
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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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58A ASP 3.6 4.7 + - - -
59A ASN* 3.5 32.6 - - - +
60A GLU 4.3 4.1 + - - +
61A THR 4.0 0.4 - - - -
62A SER* 1.3 73.8 - - - +
64A ALA* 1.3 66.4 + - - +
66A LEU* 3.2 7.1 + - - +
67A SER* 3.1 26.7 + - - +
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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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62A SER 3.5 0.6 - - - -
63A ALA* 1.3 77.4 - - - +
65A PHE* 1.3 62.4 + - + +
67A SER* 3.3 16.0 + - - -
68A LYS* 3.4 17.8 + - - +
236A ARG* 3.8 45.3 - - + +
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Residues in contact with PHE 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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57A TYR* 3.4 36.6 - + + -
62A SER* 3.8 12.9 + - - +
63A ALA 3.4 0.2 - - - -
64A ALA* 1.3 74.7 - - + +
66A LEU* 1.3 60.8 + - - +
68A LYS* 3.0 7.3 + - - +
69A ALA* 2.8 30.4 + - - +
234A MET* 3.6 42.0 - - + +
235A ASP* 4.3 5.8 - - - -
236A ARG* 3.5 28.3 - - + -
264A ARG* 4.6 4.7 - - + -
265A PRO* 4.3 9.6 - - + -
557E SER 3.1 24.7 - - - -
558E ASP* 3.1 24.2 - - - -
560E ASN* 4.5 7.9 - - + -
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Residues in contact with LEU 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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54A CYS* 3.6 25.4 - - + +
57A TYR* 3.3 25.7 - - + +
58A ASP* 3.7 2.9 - - - -
59A ASN* 3.5 50.0 - - - +
62A SER 3.3 16.1 + - - +
63A ALA 3.2 6.4 + - - +
65A PHE* 1.3 77.7 - - - +
67A SER* 1.3 56.2 + - - +
69A ALA* 3.7 2.6 - - - +
70A THR* 2.5 43.6 + - - +
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Residues in contact with SER 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 ALA 3.1 13.9 + - - -
64A ALA* 3.4 11.2 - - - -
65A PHE 3.1 0.2 - - - -
66A LEU* 1.3 74.7 - - - +
68A LYS* 1.3 59.4 + - - +
70A THR* 3.1 6.1 + - - -
71A GLU* 2.8 36.9 + - - +
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Residues in contact with LYS 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 3.6 12.1 - - - +
65A PHE* 3.0 7.5 + - - +
67A SER* 1.3 82.7 - - - +
69A ALA* 1.3 62.5 + - - +
70A THR 3.2 0.2 + - - -
71A GLU* 3.2 16.3 + - - +
72A LEU* 2.9 34.2 + - + +
233A TYR 5.0 1.6 + - - -
234A MET* 3.8 22.0 - - + -
235A ASP* 2.6 45.9 + - - +
236A ARG 4.3 1.1 - - - -
237A THR 2.8 26.1 + - - -
238A ALA* 5.3 0.7 - - - +
239A ALA* 4.4 18.8 - - - +
243A GLY* 5.2 8.0 - - - -
244A TRP* 4.7 2.2 - - - -
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Residues in contact with ALA 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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50A PHE* 3.3 28.2 - - - -
53A LEU* 4.2 13.2 - - + -
54A CYS* 3.5 33.0 - - - -
57A TYR* 4.5 2.9 - - + -
65A PHE 2.8 19.1 + - - +
66A LEU* 3.7 8.1 - - - +
68A LYS* 1.3 72.0 - - - +
70A THR* 1.3 60.2 + - - +
72A LEU* 4.7 0.7 - - - -
73A SER* 3.3 5.4 + - - -
234A MET* 4.2 13.3 - - + -
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Residues in contact with THR 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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54A CYS* 4.3 7.6 - - - -
66A LEU* 2.5 35.7 + - - +
67A SER* 3.1 4.9 + - - -
69A ALA* 1.3 73.3 - - - +
71A GLU* 1.3 66.3 + - - +
73A SER* 2.5 26.6 + - - +
74A GLU* 3.8 7.6 + - - +
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Residues in contact with GLU 71 (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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67A SER 2.8 17.0 + - - +
68A LYS* 3.6 15.2 - - - +
70A THR* 1.3 77.1 - - - +
72A LEU* 1.3 65.1 + - + +
74A GLU* 3.2 34.9 + - - +
75A VAL* 4.2 4.3 + - - +
241A ASN* 5.3 1.4 - - - +
242A GLY* 3.9 23.5 + - - -
243A GLY* 3.8 19.4 + - - -
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Residues in contact with LEU 72 (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 PHE* 3.6 23.8 - - + -
68A LYS* 2.9 22.4 + - + +
71A GLU* 1.3 81.0 - - + +
73A SER* 1.3 50.8 + - - +
74A GLU 3.1 0.4 - - - -
75A VAL* 2.9 11.7 + - + +
76A TYR* 2.8 44.9 + - + +
232A GLU* 3.7 30.7 - - + +
234A MET* 4.5 15.0 - - + -
242A GLY 4.2 14.4 - - - +
243A GLY* 5.7 1.8 - - - -
262A LEU* 3.8 30.3 - - + -
271A ILE* 5.2 0.7 - - + -
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Residues in contact with SER 73 (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 PHE* 3.6 28.2 - - - -
51A SER* 5.5 2.2 - - - -
54A CYS* 4.9 6.1 - - - -
69A ALA 3.3 6.8 + - - -
70A THR* 2.5 29.5 + - - +
72A LEU* 1.3 74.4 - - - +
74A GLU* 1.3 61.4 + - - +
75A VAL 3.3 0.2 - - - -
76A TYR 3.6 10.2 - - - +
274A LYS* 2.9 26.2 + - - -
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Residues in contact with GLU 74 (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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70A THR 4.1 7.6 - - - +
71A GLU* 3.4 26.9 - - - +
72A LEU 3.1 0.8 - - - -
73A SER* 1.3 80.4 + - - +
75A VAL* 1.3 63.2 + - + +
274A LYS* 3.7 15.3 + - - +
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Residues in contact with VAL 75 (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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71A GLU 4.6 7.4 - - - +
72A LEU* 2.9 7.0 + - + +
74A GLU* 1.3 83.1 - - + +
76A TYR* 1.3 82.5 + - + +
273A LYS* 3.7 24.2 - - + +
274A LYS* 2.9 27.4 + - - +
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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