Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 1KQN
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 PRO 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 3.5 10.3 - - - +
61A ILE* 1.3 92.3 - - + +
63A ALA* 1.3 64.9 + - - +
64A TYR* 4.4 6.7 - - + +
65A HIS* 3.2 35.3 + - + +
66A ARG* 3.4 10.2 + - - +
261A ARG* 3.9 25.5 - - - +
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Residues in contact with ALA 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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50A PRO* 5.2 0.4 - - + +
51A VAL 4.2 3.6 - - - +
53A ASP* 3.0 25.0 + - - +
62A PRO* 1.3 72.9 - - - +
64A TYR* 1.3 59.0 + - - +
66A ARG* 3.2 25.9 + - - +
67A VAL* 2.8 34.9 + - - +
87A SER* 4.0 32.1 - - - +
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Residues in contact with TYR 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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62A PRO* 3.2 6.6 - - + +
63A ALA* 1.3 79.8 - - - +
65A HIS* 1.3 64.0 + + + +
67A VAL* 3.4 12.1 + - + +
68A ILE* 3.0 67.3 + - + +
88A LEU* 6.6 0.4 - - + -
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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 ILE* 4.0 13.7 - - + -
62A PRO* 3.2 35.0 + - + +
63A ALA 3.2 0.6 - - - -
64A TYR* 1.3 82.3 - + + +
66A ARG* 1.3 60.9 + - - +
68A ILE* 3.1 3.9 + - - +
69A MET* 2.8 34.5 + - - +
247A TYR* 2.6 34.8 + + + -
251A HIS* 5.0 9.9 - + + -
253A LEU* 3.5 33.2 - - + +
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Residues in contact with ARG 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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16A SER 3.0 28.1 + - - +
17A PHE* 3.5 20.2 - - + +
18A ASN* 3.7 13.5 - - - +
20A ILE* 5.5 0.3 - - - +
50A PRO* 3.9 12.7 - - + +
51A VAL* 2.7 41.6 + - - +
52A GLY 4.0 0.2 - - - -
53A ASP* 3.2 24.5 + - - -
60A LEU* 3.2 27.7 - - - +
61A ILE* 2.8 32.1 + - + -
62A PRO 3.4 1.0 + - - +
63A ALA* 3.2 16.5 + - - +
65A HIS* 1.3 76.6 - - - +
67A VAL* 1.3 61.9 + - - +
69A MET* 3.5 14.1 + - + +
70A ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO* 4.2 21.3 - - + -
63A ALA 2.8 21.2 + - - +
64A TYR* 3.6 15.7 - - + +
66A ARG* 1.3 76.4 - - - +
68A ILE* 1.3 67.3 + - + +
70A ALA* 3.2 4.4 + - - +
71A GLU* 3.0 42.7 + - + +
82A VAL* 4.4 2.9 - - + -
84A THR* 3.9 24.0 - - + -
87A SER* 3.5 30.7 - - - +
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Residues in contact with ILE 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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64A TYR* 3.0 56.8 + - + +
65A HIS 3.5 6.3 - - - +
67A VAL* 1.3 78.2 - - + +
69A MET* 1.3 58.7 + - - +
71A GLU* 3.2 10.8 + - - +
72A LEU* 2.8 41.2 + - + +
247A TYR* 3.5 43.7 - - + +
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Residues in contact with MET 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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17A PHE 4.5 0.2 - - - +
19A PRO* 3.8 16.8 - - + -
20A ILE* 3.9 14.4 - - + -
61A ILE* 4.0 9.4 - - + -
65A HIS 2.8 18.4 + - - +
66A ARG* 3.6 29.6 - - + +
67A VAL 3.3 0.2 - - - -
68A ILE* 1.3 71.7 - - - +
70A ALA* 1.3 51.6 + - - +
72A LEU* 3.2 6.5 + - - -
73A ALA* 2.8 34.7 + - - +
244A VAL* 3.4 15.3 - - + +
247A TYR* 3.9 18.4 - - + -
248A ILE* 3.6 30.7 - - - -
253A LEU* 4.0 8.5 - - + -
254A TYR* 3.5 22.7 - - - +
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Residues in contact with ALA 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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17A PHE* 5.6 1.3 - - + -
20A ILE* 4.1 19.7 - - + +
48A ILE* 4.0 20.2 - - + -
50A PRO* 4.6 4.5 - - + -
66A ARG 3.2 13.1 + - - +
67A VAL 3.6 6.7 - - - +
68A ILE 3.2 0.2 - - - -
69A MET* 1.3 73.6 - - - +
71A GLU* 1.3 61.8 + - - +
73A ALA* 3.4 2.6 + - - +
74A THR* 2.7 32.2 + - - +
82A VAL* 3.5 21.9 - - + +
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Residues in contact with GLU 71 (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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67A VAL* 3.0 30.2 + - + +
68A ILE* 3.6 10.1 - - - +
70A ALA* 1.3 74.0 - - - +
72A LEU* 1.3 69.4 + - + +
74A THR* 3.3 7.3 + - - -
75A LYS* 3.0 24.1 + - - +
82A VAL* 3.6 30.2 - - + +
84A THR* 4.8 5.0 - - - +
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Residues in contact with LEU 72 (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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68A ILE* 2.8 25.2 + - + +
69A MET* 3.5 9.2 - - - +
71A GLU* 1.3 76.8 - - + +
73A ALA* 1.3 61.0 + - - +
75A LYS* 3.2 26.5 + - + +
76A ASN* 4.9 0.3 + - - +
241A PRO* 5.5 1.0 - - - +
243A LEU* 4.0 45.6 - - + +
244A VAL* 4.2 6.3 - - + -
247A TYR* 3.7 41.7 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.9 28.5 - - + -
25A LEU* 4.0 19.5 - - + +
69A MET 2.8 17.2 + - - +
70A ALA* 3.6 7.0 - - - +
71A GLU 3.2 0.2 - - - -
72A LEU* 1.3 77.2 - - - +
74A THR* 1.3 59.4 + - - +
75A LYS 3.4 0.4 + - - -
76A ASN 4.9 2.3 + - - -
241A PRO* 4.0 19.5 - - + +
244A VAL* 3.9 11.2 - - + +
238B TYR* 4.5 7.1 + - - -
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Residues in contact with THR 74 (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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25A LEU* 4.1 10.1 - - + -
48A ILE* 3.9 14.4 - - + -
70A ALA 2.7 22.9 + - - +
71A GLU* 3.6 5.6 + - - -
72A LEU 3.2 0.2 - - - -
73A ALA* 1.3 78.9 - - + +
75A LYS* 1.3 65.7 + - - +
76A ASN 3.1 3.1 - - - -
77A SER* 3.0 25.1 + - - +
80A VAL* 3.6 44.7 + - + +
81A GLU* 4.5 2.4 - - - +
82A VAL* 3.7 12.6 - - + +
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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