Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 3EE6
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 ASN 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN 4.3 0.2 + - - -
56A GLN* 1.3 82.4 - - - +
58A VAL* 1.3 59.0 + - - +
59A GLU 3.2 3.4 - - - -
60A ARG* 3.0 22.1 + - + +
61A LEU* 2.9 26.0 + - - +
87A ASP 5.2 0.5 - - - +
88A LEU* 2.9 39.4 - - + +
89A VAL* 5.4 0.2 - - - -
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Residues in contact with VAL 58 (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 GLN* 4.0 39.7 - - + +
56A GLN 4.1 1.8 - - - +
57A ASN* 1.3 77.7 - - - +
59A GLU* 1.3 56.9 + - - +
61A LEU* 3.2 9.5 + - + +
62A SER* 3.0 24.0 + - - -
89A VAL* 5.1 2.0 - - + -
342A THR* 3.9 30.1 - - + +
345A MET* 4.2 10.8 - - + +
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Residues in contact with GLU 59 (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 ASN 3.2 1.0 - - - -
58A VAL* 1.3 75.9 - - - +
60A ARG* 1.3 95.2 + - - +
62A SER* 3.4 9.9 + - - -
63A GLU* 3.2 28.7 + - + +
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Residues in contact with ARG 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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57A ASN* 3.0 33.9 + - + +
59A GLU* 1.3 106.3 + - - +
61A LEU* 1.3 64.0 - - - +
63A GLU* 3.1 40.6 + - - +
64A LEU* 2.9 34.5 + - + +
88A LEU* 4.1 8.7 - - + -
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Residues in contact with LEU 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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57A ASN 2.9 11.1 + - - +
58A VAL* 3.3 11.7 - - + +
60A ARG* 1.3 75.9 - - - +
62A SER* 1.3 63.4 - - - +
64A LEU* 3.3 4.6 + - + +
65A VAL* 3.0 27.9 + - - +
80A LEU* 5.4 0.4 - - + -
85A VAL* 5.3 6.3 - - + -
88A LEU* 3.9 23.5 - - + +
89A VAL* 4.6 9.0 - - + -
342A THR* 3.8 18.2 - - + +
345A MET* 3.7 30.7 - - + +
346A LYS* 3.8 26.2 - - + -
349A ALA* 4.0 25.6 - - + -
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Residues in contact with SER 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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58A VAL* 3.0 13.6 + - - -
59A GLU* 3.5 15.0 - - - -
60A ARG 3.1 0.2 - - - -
61A LEU* 1.3 77.5 - - - +
63A GLU* 1.3 62.4 + - - +
65A VAL* 3.3 12.4 + - - +
66A GLN* 3.3 13.9 + - - +
345A MET* 4.0 21.8 - - - -
384A TYR* 3.8 13.0 + - - -
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Residues in contact with GLU 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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59A GLU* 3.2 13.7 + - + +
60A ARG* 3.1 49.8 + - - +
62A SER* 1.3 76.9 - - - +
64A LEU* 1.3 68.4 + - + +
66A GLN* 3.4 8.1 + - - +
67A ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 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 ARG* 2.9 22.9 + - + +
61A LEU* 3.6 6.5 - - + +
63A GLU* 1.3 80.6 - - + +
65A VAL* 1.3 65.0 + - + +
67A ALA* 3.4 8.8 + - + +
68A VAL* 3.1 28.9 + - + +
80A LEU* 4.3 29.4 - - + -
88A LEU* 4.0 28.0 - - + -
349A ALA* 5.5 2.7 - - + -
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Residues in contact with VAL 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 LEU* 3.0 21.0 + - + +
62A SER* 3.6 8.7 - - - +
63A GLU 3.3 0.6 - - - -
64A LEU* 1.3 76.5 - - - +
66A GLN* 1.3 53.6 + - - +
68A VAL* 3.2 8.0 + - - +
69A SER* 2.7 47.2 + - - +
345A MET* 3.3 39.3 - - + +
348A ALA* 4.0 19.3 - - + -
349A ALA* 4.1 11.7 - - + +
384A TYR* 3.9 25.1 - - + -
502A PHE* 4.3 3.4 - - + -
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Residues in contact with GLN 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 SER 3.3 9.3 + - - +
63A GLU* 3.9 9.2 - - - +
64A LEU 3.3 0.4 - - - -
65A VAL* 1.3 81.0 - - + +
67A ALA* 1.3 58.0 + - - +
69A SER* 3.8 6.1 - - - -
70A ASP* 2.9 57.2 + - + +
420A SER* 5.4 6.3 + - - -
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Residues in contact with ALA 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 GLU 3.1 18.8 + - - +
64A LEU* 3.7 13.5 - - + +
65A VAL 3.2 0.2 - - - -
66A GLN* 1.3 77.1 - - - +
68A VAL* 1.3 58.2 + - + +
73A SER* 2.4 38.2 + - - +
75A GLN* 3.1 27.8 - - + +
76A TYR 3.3 0.5 + - - -
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Residues in contact with VAL 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 LEU 3.1 15.3 + - - +
65A VAL* 3.9 6.3 - - - +
67A ALA* 1.3 79.3 - - + +
69A SER* 1.3 61.5 + - - +
70A ASP 3.7 0.2 - - - -
75A GLN* 3.5 13.2 - - + +
76A TYR* 3.9 3.5 - - - -
77A GLY* 3.0 21.5 + - - -
78A LYS* 2.8 38.6 - - + +
79A TYR* 3.3 33.8 + - + +
80A LEU* 4.8 8.5 - - + -
348A ALA 4.0 8.3 - - - +
349A ALA* 4.0 13.0 - - - +
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Residues in contact with SER 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 VAL* 2.7 25.0 + - - +
66A GLN* 3.8 5.0 - - - -
68A VAL* 1.3 83.8 - - - +
70A ASP* 1.3 60.4 + - - +
71A PRO* 3.5 10.4 - - - +
76A TYR* 3.9 11.9 - - - -
79A TYR* 5.5 2.2 - - - -
348A ALA 5.7 1.1 - - - -
500A LEU 6.1 0.2 - - - -
502A PHE* 3.8 45.6 - - - +
505A PRO* 3.5 17.7 - - - +
506A ARG* 4.6 2.4 + - - +
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Residues in contact with ASP 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 GLN* 2.9 40.9 + - + +
68A VAL 3.7 0.4 - - - +
69A SER* 1.3 76.5 - - - +
71A PRO* 1.3 62.9 - - - +
72A SER* 2.5 32.2 + - - -
73A SER* 2.7 41.1 + - - -
76A TYR* 3.6 5.5 - - - +
505A PRO* 4.5 8.6 - - + +
509A GLN* 4.2 5.9 + - - -
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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