Contacts of the helix formed by residues 56 - 69 (chain A) in PDB entry 1TQN
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 GLY 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER 4.7 0.3 - - - +
53A TYR* 2.8 17.5 + - - +
55A LYS* 1.3 80.8 + - - +
57A PHE* 1.3 66.6 + - - -
58A CYS 3.4 1.8 - - - -
59A MET 3.6 0.6 + - - -
60A PHE* 3.3 21.7 + - - +
216A LEU* 3.9 4.0 - - - -
478A SER 5.5 0.7 - - - -
479A LEU* 3.3 16.3 + - - -
480A GLY 3.7 9.0 - - - -
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Residues in contact with PHE 57 (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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53A TYR* 3.4 43.3 - + - -
56A GLY* 1.3 71.9 - - - -
58A CYS* 1.3 60.3 + - - +
60A PHE* 3.1 4.9 + - - +
61A ASP* 2.9 32.6 + - - +
76A ASP* 5.8 0.9 - - - -
215A PHE* 4.0 26.7 - + + -
216A LEU* 3.6 19.4 - - + +
371A MET* 4.1 22.1 - - + -
372A ARG* 3.5 32.3 - - - +
480A GLY 4.4 1.2 + - - -
481A GLY* 3.6 38.6 - - - -
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Residues in contact with CYS 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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56A GLY 3.4 0.8 - - - -
57A PHE* 1.3 72.3 - - - +
59A MET* 1.3 73.8 + - + +
61A ASP* 3.4 7.3 + - - +
62A MET* 2.9 32.0 + - - +
371A MET* 3.5 33.9 - - - -
399A TYR* 3.2 53.8 - - + -
477A LEU* 5.9 0.2 - - + -
483A LEU* 4.7 9.0 - - + -
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Residues in contact with MET 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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55A LYS* 3.3 44.9 - - + +
56A GLY 3.6 1.4 + - - +
57A PHE 3.3 0.4 - - - -
58A CYS* 1.3 91.4 - - + +
60A PHE* 1.3 64.6 + - - +
62A MET* 3.3 8.8 + - + +
63A GLU* 3.0 38.4 + - + +
399A TYR* 4.0 22.2 - - + +
477A LEU* 4.5 14.6 - - + -
479A LEU* 5.6 3.1 - - + -
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Residues in contact with PHE 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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41A PRO* 4.2 10.8 - - + -
49A ASN* 4.6 6.3 - - + -
52A SER* 3.6 43.5 + - - +
53A TYR* 3.5 14.8 - + + -
55A LYS* 5.8 0.2 - - - +
56A GLY 3.3 12.2 + - - +
57A PHE 3.1 7.5 + - - +
59A MET* 1.3 81.1 - - - +
61A ASP* 1.3 59.0 + - - +
63A GLU* 3.4 9.2 + - + +
64A CYS* 3.0 53.3 + - - -
74A PHE* 3.8 48.2 - + + -
372A ARG* 3.5 23.1 - - - -
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Residues in contact with ASP 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 PHE 2.9 18.6 + - - +
58A CYS* 3.9 6.8 - - - +
59A MET 3.3 0.2 - - - -
60A PHE* 1.3 80.4 - - - +
62A MET* 1.3 61.4 + - - +
64A CYS* 4.5 3.6 - - - +
65A HIS* 3.0 28.8 + - - +
72A TRP* 3.7 8.8 + - + -
74A PHE* 4.8 0.3 - - - -
371A MET 4.7 1.9 - - - +
372A ARG* 2.8 53.8 + - - +
395A MET* 3.4 14.6 - - - +
397A PRO* 3.7 20.2 - - + +
399A TYR* 5.8 1.3 - - + +
400A ALA* 4.0 9.0 - - + +
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Residues in contact with MET 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 CYS 2.9 25.7 + - - +
59A MET* 3.8 11.4 - - + +
61A ASP* 1.3 72.8 - - - +
63A GLU* 1.3 68.1 + - + +
65A HIS* 3.3 5.6 + - - +
66A LYS* 3.0 24.1 + - - +
399A TYR* 3.7 24.2 - - + +
400A ALA* 2.9 47.1 - - + +
403A ARG* 3.8 20.4 - - + +
404A ASP* 5.5 0.9 - - - -
412A GLU* 5.7 2.0 - - - +
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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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55A LYS* 5.0 13.0 + - - +
59A MET* 3.0 27.0 + - + +
60A PHE* 3.9 7.2 - - + +
62A MET* 1.3 76.7 - - + +
64A CYS* 1.3 65.4 + - - +
66A LYS* 3.0 42.2 + - + +
67A LYS* 3.1 16.2 + - + +
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Residues in contact with CYS 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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41A PRO* 4.3 4.7 - - - -
60A PHE* 3.0 54.9 + - - +
63A GLU* 1.3 75.8 - - - +
65A HIS* 1.3 61.8 + - - +
67A LYS* 5.1 0.4 - - - -
68A TYR* 2.8 57.9 + - + +
72A TRP* 3.2 36.5 - - + +
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Residues in contact with HIS 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 ASP 3.0 18.6 + - - +
62A MET* 3.5 9.0 - - - +
64A CYS* 1.3 76.5 - - - +
66A LYS* 1.3 63.9 + - - +
69A GLY* 3.1 46.7 + - - +
70A LYS* 5.1 0.6 - - - -
72A TRP* 3.4 21.0 - + + -
85A THR* 3.7 17.8 + - + +
400A ALA* 4.6 14.2 + - + +
401A LEU* 4.2 12.8 - - + -
404A ASP* 3.3 38.5 + - + +
406A LYS* 6.0 0.4 - - + -
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Residues in contact with LYS 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 MET 3.0 11.8 + - - +
63A GLU* 3.0 35.3 + - + +
64A CYS 3.2 0.2 - - - -
65A HIS* 1.3 83.1 - - - +
67A LYS* 1.3 92.3 + - - +
69A GLY* 4.5 2.1 + - - -
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Residues in contact with LYS 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 20.0 + - - +
64A CYS* 5.1 0.2 - - - -
66A LYS* 1.3 101.4 - - - +
68A TYR* 1.3 104.1 + - + +
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Residues in contact with TYR 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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39A PRO* 4.0 18.9 - - + +
40A GLY* 3.6 23.2 + - - -
41A PRO* 3.3 43.3 - - + +
64A CYS* 2.8 45.3 + - + +
67A LYS* 1.3 111.8 + - + +
69A GLY* 1.3 61.3 + - - +
70A LYS 4.1 0.3 + - - -
71A VAL 3.9 7.3 - - - +
72A TRP* 3.6 23.3 - - + -
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Residues in contact with GLY 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 HIS* 3.1 34.6 + - - -
66A LYS 4.5 1.8 + - - -
67A LYS 3.7 0.8 - - - -
68A TYR* 1.3 78.8 - - - +
70A LYS* 1.3 58.8 + - - -
71A VAL 3.4 1.3 - - - -
72A TRP* 3.2 11.4 - - - -
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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