Contacts of the helix formed by residues 78 - 88 (chain L) in PDB entry 1KYO
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 78 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74L ASN 3.2 9.2 + - - -
75L ILE* 2.9 24.9 + - - -
76L PHE 3.3 0.8 - - - -
77L LEU* 1.3 78.6 - - - +
79L LYS* 1.3 61.6 + - - +
80L GLU* 3.2 6.6 + - - +
81L ASN* 3.3 5.1 + - - -
82L SER* 2.8 35.2 + - - -
130L LEU* 5.1 0.7 - - - -
135L ASN* 2.9 32.3 + - - -
139L THR* 4.3 5.9 + - - -
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Residues in contact with LYS 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU 3.9 0.2 + - - -
78L SER* 1.3 76.6 + - - +
80L GLU* 1.3 63.8 + - - +
82L SER* 4.2 1.1 - - - -
83L ALA* 3.2 21.8 + - - +
263M ALA* 3.4 39.1 - - + +
265M SER 3.4 20.7 + - - -
266M GLU* 4.1 16.8 + - - +
267M LEU 4.8 0.2 - - - +
268M SER* 4.7 7.3 + - - +
269M GLY 5.9 0.8 - - - +
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Residues in contact with GLU 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L SER* 3.4 3.4 + - - +
79L LYS* 1.3 80.6 - - - +
81L ASN* 1.3 59.3 + - - +
83L ALA* 3.9 3.3 + - - +
84L VAL* 3.3 22.7 + - - +
126L GLN* 5.0 3.5 - - - +
129L ASN* 5.8 0.3 - - - +
130L LEU* 4.5 21.9 + - + +
132L SER* 4.7 5.8 + - - -
134L SER* 5.6 1.2 - - - -
135L ASN* 3.5 38.5 + - - +
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Residues in contact with ASN 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ILE 4.3 2.7 - - - +
76L PHE* 3.8 28.3 + - - +
78L SER* 3.3 4.4 + - - +
80L GLU* 1.3 78.3 - - - +
82L SER* 1.3 64.7 + - - +
83L ALA 3.3 0.2 - - - -
84L VAL* 3.3 12.4 + - - +
85L ALA 3.4 9.4 + - - -
92L LEU* 4.0 1.9 - - - +
118L PHE* 3.5 29.0 - - + -
122L SER* 3.1 26.7 + - - -
126L GLN* 3.1 28.6 + - - +
130L LEU* 3.8 25.8 - - + +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU* 3.2 17.0 + - - +
78L SER 2.8 23.6 + - - -
79L LYS* 4.2 0.4 - - - -
80L GLU 3.4 0.2 - - - -
81L ASN* 1.3 77.9 - - - +
83L ALA* 1.3 56.0 + - - +
85L ALA* 3.5 2.4 + - - +
86L ALA* 3.0 28.9 + - - +
92L LEU* 3.8 17.0 - - - +
263M ALA* 3.5 21.0 - - - +
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Residues in contact with ALA 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L LYS 3.2 16.6 + - - +
80L GLU 4.2 4.3 - - - +
82L SER* 1.3 73.7 - - - +
84L VAL* 1.3 66.1 + - + +
86L ALA* 3.7 0.6 - - - +
87L LYS* 3.1 37.5 + - - +
263M ALA* 3.5 22.3 - - - +
264M LEU* 4.0 14.4 - - + -
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Residues in contact with VAL 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L GLU 3.3 18.4 - - - +
81L ASN* 3.3 14.7 + - - +
83L ALA* 1.3 78.5 - - + +
85L ALA* 1.3 58.0 + - - +
87L LYS* 4.5 5.2 - - - +
88L GLU* 3.7 20.3 + - - +
118L PHE* 3.7 18.6 - - + -
121L GLN* 3.8 18.4 - - - +
126L GLN* 5.1 6.3 - - - +
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Residues in contact with ALA 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L ASN 3.4 5.5 + - - +
82L SER 4.2 3.1 - - - +
83L ALA 3.2 0.4 - - - -
84L VAL* 1.3 77.9 - - - +
86L ALA* 1.3 55.3 + - - +
87L LYS 3.4 0.7 - - - -
88L GLU 3.6 1.9 + - - -
89L GLY 3.1 7.1 + - - -
90L LEU* 2.6 58.6 + - + +
92L LEU* 4.0 16.6 - - + -
118L PHE* 3.5 29.6 - - + -
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L SER 3.0 19.6 + - - +
83L ALA* 3.2 0.9 + - - -
85L ALA* 1.3 75.1 - - - +
87L LYS* 1.3 66.9 + - - +
89L GLY 3.0 8.3 + - - -
90L LEU 4.0 9.0 - - - -
262M SER* 5.0 3.8 - - - -
263M ALA 5.4 0.7 - - - +
264M LEU* 3.6 31.2 - - + +
316M PRO 4.1 2.4 - - - +
320M TYR* 3.4 36.8 - - + +
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Residues in contact with LYS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L ALA* 3.1 20.9 + - - +
84L VAL* 4.5 4.9 - - - +
86L ALA* 1.3 76.6 - - - +
88L GLU* 1.3 60.0 - - - +
89L GLY* 2.9 7.8 + - - -
264M LEU* 3.8 17.5 - - + -
316M PRO* 4.0 32.0 - - + +
318M ILE 4.6 5.4 - - - +
319M ASN* 4.8 4.0 - - - +
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Residues in contact with GLU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L VAL 3.7 17.9 + - - +
85L ALA 3.6 5.6 + - - +
86L ALA 3.3 0.4 - - - -
87L LYS* 1.3 79.0 - - - +
89L GLY* 1.3 60.7 - - - +
90L LEU* 3.6 20.5 - - + +
111L SER* 5.4 2.8 + - - -
114L LYS* 3.1 50.4 + - + +
118L PHE* 6.0 1.6 - - + -
319M ASN* 5.7 1.5 - - - +
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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