Contacts of the helix formed by residues 65 - 70 (chain A) in PDB entry 1KT8
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.4 10.7 - - - +
62A HIS* 2.9 21.7 + - - -
63A PRO 3.4 1.2 - - - -
64A ALA* 1.3 75.4 - - - +
66A SER* 1.3 58.5 + - - +
67A SER* 2.9 22.7 + - - -
68A LEU* 2.8 25.1 + - - +
69A HIS* 3.3 10.4 - - - -
149A ASN* 2.8 29.5 + - - -
150A GLU 3.5 10.5 - - - -
151A PRO* 4.5 1.1 - - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 3.1 7.3 + - - -
65A SER* 1.3 70.7 + - - +
67A SER* 1.3 60.6 + - - +
68A LEU 3.1 0.2 - - - -
69A HIS* 3.9 3.1 - - - +
70A TYR* 3.0 37.0 + - - +
72A LEU* 3.5 38.2 + - - +
148A GLY* 3.6 0.9 - - - -
149A ASN 3.5 8.7 + - - -
150A GLU* 3.2 27.5 + - - +
152A SER 4.9 4.5 - - - -
154A GLY 5.6 2.0 - - - -
156A SER 5.5 1.6 - - - -
158A PRO* 4.1 4.5 - - - +
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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
----------------------------------------------------------
61A LEU* 4.0 1.7 - - - +
65A SER* 2.9 18.8 + - - -
66A SER* 1.3 77.6 - - - +
68A LEU* 1.3 63.8 + - - +
71A SER* 3.9 3.2 - - - -
72A LEU 3.8 12.3 - - - +
73A GLN* 3.2 13.3 - - - +
147A ILE* 3.7 25.0 - - - +
148A GLY 3.1 22.3 + - - -
568B LEU* 3.5 20.0 - - - +
573B GLN* 2.9 17.8 + - - +
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Residues in contact with LEU 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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61A LEU* 4.3 8.5 - - + -
62A HIS 4.9 2.2 - - - +
63A PRO 5.1 1.1 - - - +
65A SER* 2.8 14.3 + - - +
67A SER* 1.3 86.8 + - - +
69A HIS* 1.3 65.5 - - + +
559B LEU* 3.5 32.3 - - + -
561B LEU* 4.0 15.0 - - + -
567B SER* 3.6 33.4 - - - +
568B LEU* 3.6 18.6 - - + -
573B GLN* 3.2 29.1 + - - +
574B LEU 5.3 1.0 + - - +
645B VAL* 4.4 9.7 - - - +
647B ILE* 4.1 13.7 - - + -
664B PHE* 4.7 7.4 - - + -
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Residues in contact with HIS 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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63A PRO 2.7 25.8 + - - -
64A ALA* 3.4 14.1 - - - +
65A SER 3.3 18.7 + - - +
66A SER* 4.7 1.1 - - - -
68A LEU* 1.3 85.7 - - + +
70A TYR* 1.3 84.3 + - + +
153A LEU* 3.8 10.7 - - + +
573B GLN* 3.5 3.1 - - - -
575B PHE* 3.5 15.0 - - - +
643B ARG* 3.0 44.8 + - + +
645B VAL* 3.3 30.4 - - + +
664B PHE* 4.1 3.0 - - - -
666B ILE* 4.1 3.8 - - + -
704B GLY* 3.3 16.1 - - - -
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Residues in contact with TYR 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 SER* 3.0 21.2 + - - +
69A HIS* 1.3 104.0 - - + +
71A SER* 1.3 66.2 + - - +
72A LEU* 3.1 13.0 + - + +
152A SER 4.5 2.7 - - - -
153A LEU* 2.5 38.5 + - - -
154A GLY 3.8 8.5 - - - -
155A VAL* 3.6 22.2 - - + -
156A SER 5.3 0.7 - - - -
575B PHE* 3.7 18.4 - + - -
643B ARG* 2.8 26.7 + - - -
704B GLY 3.5 7.2 - - - -
707B TYR* 3.9 21.8 - - + -
708B GLY* 3.0 24.7 + - - +
711B VAL* 6.2 0.4 - - + -
900B ILP 2.9 26.5 - - + +
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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