Contacts of the helix formed by residues 68 - 77 (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 VAL 68 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61L GLU* 3.5 18.2 - - - +
65L ASN* 3.3 21.6 + - - +
67L GLY* 1.3 78.1 - - - +
69L SER* 1.3 64.9 + - - +
71L LEU* 3.0 18.3 + - - +
72L TRP* 3.0 16.6 + - + -
187L LEU* 3.7 10.8 - - + -
191L ASP* 4.1 12.3 - - + +
192L LEU* 4.0 37.5 - - + +
195L PHE* 3.7 33.2 - - + -
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Residues in contact with SER 69 (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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57L GLY 4.3 4.0 - - - -
61L GLU* 2.8 21.1 + - - -
68L VAL* 1.3 76.6 - - - +
70L ASN* 1.3 60.9 + - - +
71L LEU 3.0 4.9 - - - -
72L TRP* 3.0 7.5 + - - +
73L LYS 3.0 19.9 + - - -
96L ILE* 3.3 28.3 - - - +
101L GLN* 3.1 34.4 + - - -
177L THR 5.6 0.4 - - - -
195L PHE* 3.4 14.4 - - - -
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Residues in contact with ASN 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L GLY 3.9 5.4 + - - +
68L VAL 3.3 0.2 - - - -
69L SER* 1.3 79.7 - - - +
71L LEU* 1.3 58.6 + - - +
73L LYS* 3.6 14.4 - - - +
74L ASN* 2.8 43.6 + - - +
96L ILE* 3.9 13.2 - - + +
143L VAL* 4.5 10.9 - - - +
146L GLN* 4.3 12.3 + - - +
147L VAL* 4.0 11.1 - - - +
177L THR 3.7 20.5 + - - +
178L ARG* 3.2 38.5 + - - +
184L LEU* 5.0 1.0 - - - +
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Residues in contact with LEU 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L GLY 3.3 12.0 + - - +
68L VAL* 3.0 12.3 + - - +
69L SER 3.0 0.4 - - - -
70L ASN* 1.3 78.2 - - - +
72L TRP* 1.3 61.5 + - - +
74L ASN* 3.6 2.0 + - - +
75L ILE* 3.3 26.5 + - - +
136L PHE* 4.1 15.5 - - + -
139L THR* 4.5 5.4 - - + -
140L LYS* 4.2 20.2 - - + +
143L VAL* 3.6 33.9 - - + -
184L LEU* 4.9 7.2 - - + +
187L LEU* 3.8 28.0 - - + -
192L LEU* 3.8 28.5 - - + -
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Residues in contact with TRP 72 (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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68L VAL* 3.0 17.9 + - + -
69L SER* 3.0 6.0 + - - +
71L LEU* 1.3 73.0 - - - +
73L LYS* 1.3 64.5 + - - +
75L ILE* 2.9 41.2 + - + +
76L PHE* 2.9 25.8 + - + +
101L GLN* 4.3 0.7 - - - +
103L TYR* 3.0 26.6 - + - +
123L PHE* 6.0 0.2 - + - -
127L LYS* 3.4 39.9 - - + -
130L LEU* 5.9 1.8 - - + -
131L LEU* 4.1 21.3 - - + -
192L LEU* 3.1 57.0 + - + +
193L GLU* 4.4 1.6 - - - -
195L PHE* 4.4 11.3 - + - +
196L ALA* 3.4 17.5 - - + +
200L PHE* 3.7 23.3 - + - -
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Residues in contact with LYS 73 (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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69L SER 3.0 6.8 + - - +
70L ASN* 3.6 24.0 - - - +
72L TRP* 1.3 77.0 - - - +
74L ASN* 1.3 66.8 + - - +
76L PHE* 3.7 1.6 + - - +
77L LEU* 3.0 45.6 + - + +
94L SER* 2.9 57.0 + - - +
95L ASN* 3.7 10.9 - - - +
96L ILE* 3.6 27.4 - - + +
103L TYR* 3.6 5.5 + - - -
146L GLN* 5.7 2.9 - - - -
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Residues in contact with ASN 74 (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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70L ASN* 2.8 38.8 + - - +
71L LEU 3.6 1.5 + - - +
72L TRP 3.1 0.8 - - - -
73L LYS* 1.3 88.7 - - - +
75L ILE* 1.3 58.8 + - - +
77L LEU* 3.6 10.3 - - - +
78L SER* 3.2 20.8 + - - -
139L THR* 3.6 15.7 - - + +
142L SER* 6.0 0.9 - - - -
143L VAL* 3.4 30.1 - - + +
146L GLN* 3.1 24.8 + - - +
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Residues in contact with ILE 75 (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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71L LEU* 3.3 15.3 - - + +
72L TRP* 2.9 49.9 + - + +
74L ASN* 1.3 73.9 - - - +
76L PHE* 1.3 69.2 + - - +
77L LEU 3.0 1.3 - - - -
78L SER* 2.9 29.2 + - - -
81L ASN* 4.3 5.7 - - - +
130L LEU* 4.3 29.0 - - + +
131L LEU* 4.0 17.9 - - + +
135L ASN* 4.7 8.5 - - - +
136L PHE* 4.8 17.3 - - + -
139L THR* 3.5 23.6 - - + +
192L LEU* 5.2 3.1 - - + -
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Residues in contact with PHE 76 (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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72L TRP* 2.9 18.2 + - + +
73L LYS 3.9 2.0 - - - +
75L ILE* 1.3 83.0 - - + +
77L LEU* 1.3 69.7 + - + +
78L SER 3.3 1.6 + - - -
81L ASN* 3.8 19.5 + - - +
92L LEU* 3.6 47.4 - - + +
93L SER 4.6 1.1 - - - -
94L SER* 4.5 1.6 - - - -
103L TYR* 3.4 44.9 - + + -
104L ILE 4.4 7.0 - - - -
105L VAL* 4.2 12.6 - - + -
118L PHE* 4.6 5.8 - + - -
119L LEU* 5.3 3.8 - - + -
122L SER* 4.6 13.2 - - - -
123L PHE* 3.7 30.1 - + - -
127L LYS* 6.0 1.3 - - - -
130L LEU* 5.4 3.4 - - + -
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Residues in contact with LEU 77 (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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73L LYS* 3.0 42.2 + - + +
74L ASN* 3.6 12.3 - - - +
75L ILE 3.0 0.4 - - - -
76L PHE* 1.3 81.8 - - + +
78L SER* 1.3 66.4 + - - +
79L LYS 3.9 0.2 + - - -
82L SER* 3.2 12.8 + - - -
92L LEU* 3.8 33.0 - - + +
93L SER* 4.2 0.2 - - - -
94L SER* 3.8 34.1 - - - +
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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