Contacts of the helix formed by residues 57 - 68 (chain D) in PDB entry 1T5A
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D PRO 5.3 1.9 + - - -
54D ALA 5.1 1.4 + - - -
55D SER* 5.1 0.3 - - - -
56D ARG* 1.3 75.1 + - - +
58D VAL* 1.3 57.3 + - - +
59D GLU* 4.2 6.3 - - - -
60D THR* 2.5 46.5 + - - +
61D LEU* 2.6 32.8 + - - -
90D ASN* 4.3 2.0 - - - +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG 3.3 4.4 + - - -
57D SER* 1.3 69.8 - - - +
59D GLU* 1.3 63.1 + - - +
61D LEU* 3.7 10.3 - - - +
62D LYS* 3.1 44.0 + - - +
90D ASN* 2.9 49.3 - - + +
93D THR* 4.0 25.8 - - + +
94D ALA* 3.8 6.9 - - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D SER* 2.7 10.4 + - - -
58D VAL* 1.3 81.7 - - - +
60D THR* 1.3 79.4 + - + +
62D LYS* 3.4 20.6 + - - +
63D GLU* 3.8 9.7 + - + +
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA 4.1 7.1 + - - +
55D SER* 3.8 19.5 - - - -
57D SER* 2.5 33.6 + - - +
59D GLU* 1.3 86.0 - - - +
61D LEU* 1.3 53.2 + - - -
62D LYS 3.0 5.6 - - - -
63D GLU* 2.8 31.6 + - - +
64D MET* 3.0 16.3 + - - +
371D PRO* 6.4 1.1 - - - -
372D LEU* 4.3 7.0 - - - +
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 4.0 23.3 - - + -
55D SER 3.1 20.0 - - - +
56D ARG* 4.0 9.2 - - - +
57D SER 2.6 18.6 + - - +
58D VAL* 3.7 7.6 - - - +
60D THR* 1.3 71.8 + - - +
62D LYS* 1.3 59.9 + - - +
63D GLU 3.3 0.2 - - - -
64D MET* 3.6 13.5 - - + +
65D ILE* 3.4 25.4 + - + +
69D MET* 4.2 10.3 - - + -
87D THR* 4.6 0.7 - - + +
90D ASN* 3.6 16.2 - - + -
91D VAL* 3.4 46.4 - - + +
94D ALA* 3.9 5.8 - - + -
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 3.1 37.9 + - - +
59D GLU* 3.6 12.5 - - - +
60D THR 3.0 0.6 - - - -
61D LEU* 1.3 76.9 - - - +
63D GLU* 1.3 68.0 + - - +
64D MET 3.2 0.4 - - - -
65D ILE* 3.5 4.5 + - - +
66D LYS* 3.1 31.3 + - - +
93D THR* 6.0 0.7 - - - -
94D ALA* 3.7 16.4 - - + +
97D SER* 3.8 30.4 - - - +
98D PHE* 4.1 15.0 - - + -
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 3.9 13.5 - - + +
60D THR* 2.8 14.2 + - - +
62D LYS* 1.3 80.8 - - - +
64D MET* 1.3 57.7 + - - +
66D LYS* 3.0 39.4 - - - +
67D SER* 2.9 35.2 + - - +
372D LEU* 3.5 25.5 - - + +
376D ARG* 4.6 11.3 + - - -
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D CYS* 4.7 4.3 - - - -
51D ILE* 4.6 8.7 - - - -
55D SER* 3.8 21.5 - - - -
60D THR* 3.0 16.7 + - - +
61D LEU* 3.6 22.7 - - + +
62D LYS 3.2 0.2 - - - -
63D GLU* 1.3 78.6 - - - +
65D ILE* 1.3 60.6 + - - +
67D SER* 3.5 2.8 + - - -
68D GLY 3.1 7.3 + - - -
69D MET* 2.9 41.0 + - + +
365D THR* 4.5 7.9 - - + -
371D PRO* 3.6 35.9 - - + +
372D LEU* 3.2 27.6 - - + -
375D VAL* 3.8 20.1 - - + +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 3.4 16.8 - - + +
62D LYS 3.5 6.2 + - - +
63D GLU 3.3 0.2 - - - -
64D MET* 1.3 75.4 - - - +
66D LYS* 1.3 66.3 + - - +
68D GLY* 3.3 12.0 + - - -
69D MET* 3.6 27.7 - - + +
91D VAL* 4.8 0.9 - - + +
94D ALA* 3.9 6.3 - - + +
95D THR* 3.4 45.8 - - - +
98D PHE* 4.4 16.6 - - + -
106D ARG* 3.6 34.8 + - + +
108D VAL* 3.9 17.3 - - + -
708D GOL 4.3 0.3 + - - -
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS* 3.1 15.5 + - - +
63D GLU* 3.0 37.5 - - - +
65D ILE* 1.3 81.7 - - - +
67D SER* 1.3 63.5 + - - +
68D GLY 3.2 0.5 + - - -
98D PHE* 4.0 26.0 - - + -
106D ARG* 3.4 21.3 + - - +
708D GOL 3.2 24.6 + - - -
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLU* 2.9 21.2 + - - -
64D MET 3.9 3.6 - - - -
66D LYS* 1.3 76.7 - - - +
68D GLY* 1.3 56.4 + - - +
372D LEU* 4.1 8.4 - - - +
375D VAL* 3.8 16.0 - - - +
376D ARG* 2.9 51.1 + - - +
379D ASN* 4.1 12.1 - - - +
708D GOL 3.6 16.1 - - - -
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ARG* 3.0 24.0 + - - -
47D ILE* 4.1 3.8 - - - +
64D MET 3.1 2.2 + - - -
65D ILE 3.3 2.9 + - - -
66D LYS 3.2 3.8 - - - -
67D SER* 1.3 79.1 - - - +
69D MET* 1.3 60.0 + - - +
70D ASN* 2.7 29.3 + - - +
375D VAL* 3.9 7.2 - - - -
708D GOL 3.4 11.1 + - - -
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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