Contacts of the helix formed by residues 67 - 77 (chain U) in PDB entry 5K0Y
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 67 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U ALA* 3.7 21.1 - - + +
41U VAL* 4.8 1.1 - - - -
45U TYR* 3.9 30.7 - - + +
47U LYS* 4.2 14.1 - - + -
64U ALA 5.5 0.2 - - - +
65U GLN 3.4 8.7 - - - +
66U CYS* 1.3 89.5 - - - +
68U ILE* 1.4 65.2 + - - +
69U VAL* 3.8 22.0 - - + -
70U GLU* 3.3 21.4 + - + +
71U ARG* 3.2 19.8 + - - +
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Residues in contact with ILE 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U TYR 3.3 26.7 - - - +
39U ILE* 3.9 18.8 - - + -
40U ALA 3.6 20.5 + - - +
41U VAL* 5.5 2.5 - - + -
67U PRO* 1.4 69.1 - - - +
69U VAL* 1.4 75.5 + - + +
71U ARG* 3.5 10.1 + - - +
72U LEU* 3.0 29.3 + - - +
109U LEU* 5.4 1.1 - - + +
112U LEU* 3.5 34.0 - - + +
113U VAL* 4.2 17.5 - - + -
116U ILE* 5.3 8.7 - - + -
147U VAL* 4.0 18.2 - - + -
151U ILE* 4.1 9.6 - - + +
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Residues in contact with VAL 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U PHE* 4.6 20.4 - - + -
41U VAL* 4.2 20.0 - - + -
45U TYR 5.6 1.1 - - - +
47U LYS* 6.2 4.3 - - + +
50U PRO* 5.2 6.3 - - + -
67U PRO* 3.8 21.1 - - + -
68U ILE* 1.4 82.8 - - + +
70U GLU* 1.4 64.5 + - + +
72U LEU* 3.3 10.1 + - - +
73U THR* 3.2 26.3 + - + +
93U VAL* 5.8 0.2 - - - +
97U PHE* 4.6 8.6 - - + -
109U LEU* 4.0 22.0 - - + -
112U LEU* 3.9 22.0 - - + -
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Residues in contact with GLU 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U LYS* 4.1 4.8 - - - -
50U PRO* 3.9 18.4 - - + -
51U HIS* 3.1 30.6 + - - +
52U SER* 3.2 24.0 + - - -
56U TYR* 3.3 15.6 + - - +
66U CYS* 3.3 22.0 - - - -
67U PRO* 3.3 26.5 + - + +
69U VAL* 1.4 77.5 - - - +
71U ARG* 1.4 63.6 + - - +
73U THR* 2.8 23.2 + - - +
74U ASN* 3.1 24.6 + - - +
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Residues in contact with ARG 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671A U 5.0 9.1 + - - +
1672A U 3.7 22.2 + - - -
38U TYR* 5.5 4.2 + - - -
56U TYR* 5.8 4.2 - - - +
63U LYS* 3.2 46.7 + - - +
66U CYS* 3.4 41.2 + - - +
67U PRO 3.2 13.8 + - - +
68U ILE* 3.8 7.0 - - - +
70U GLU* 1.4 75.6 - - - +
72U LEU* 1.4 56.3 + - - +
74U ASN* 3.4 6.7 + - - +
75U SER* 3.1 43.1 + - - +
144U LEU* 5.4 4.4 - - - +
147U VAL* 5.0 5.8 - - - +
148U ASN* 3.7 23.5 + - - +
151U ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U ILE 3.0 14.5 + - - +
69U VAL* 3.4 11.0 - - - +
71U ARG* 1.4 73.5 - - - +
73U THR* 1.4 63.5 + - + +
76U MET* 3.5 22.1 + - + +
93U VAL* 5.3 10.9 - - + +
97U PHE* 5.3 9.9 - - + -
112U LEU* 3.9 37.5 - - + -
151U ILE* 3.8 23.7 - - + +
154U LEU* 5.0 6.7 - - + -
155U CYS* 3.7 29.2 - - - -
173U LEU* 4.6 29.2 - - + -
177U LEU* 4.9 1.6 - - + -
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Residues in contact with THR 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U PHE* 6.5 0.4 - - + -
50U PRO* 4.4 20.9 - - + +
69U VAL 3.2 12.4 + - - +
70U GLU* 2.8 22.7 + - - +
72U LEU* 1.4 76.7 - - + +
74U ASN* 1.4 69.2 + - - +
76U MET* 3.5 4.3 + - - +
77U MET* 4.1 4.6 + - - +
86U LYS* 5.4 6.2 - - - +
89U THR* 3.4 31.1 - - + +
90U VAL* 5.1 13.8 - - + +
93U VAL* 3.9 33.0 - - + -
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Residues in contact with ASN 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1670A A 2.9 47.2 + - - +
1671A U 3.1 24.7 + - - +
56U TYR* 3.7 25.5 + - - -
66U CYS* 4.4 1.6 - - - -
70U GLU* 3.1 27.1 + - - +
71U ARG* 3.7 7.0 - - - +
73U THR* 1.4 81.5 + - - +
75U SER* 1.4 61.3 + - - +
76U MET 3.2 1.6 + - - -
77U MET* 3.3 24.8 + - - +
78U MET* 5.6 0.3 - - - +
86U LYS* 5.0 7.4 - - - +
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Residues in contact with SER 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1671A U 3.8 27.9 + - - -
71U ARG* 3.1 21.3 + - - +
73U THR 3.5 0.4 - - - -
74U ASN* 1.4 75.0 - - - +
76U MET* 1.4 60.8 + - - +
77U MET 3.5 0.3 + - - -
78U MET* 3.6 18.1 - - - +
151U ILE* 3.6 14.4 - - - +
152U TRP* 4.2 17.4 + - - -
155U CYS* 3.9 18.2 - - - -
159U ARG* 3.7 10.0 + - - -
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Residues in contact with MET 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530A U 3.5 14.9 - - - +
72U LEU* 3.5 12.6 + - + +
73U THR* 3.6 11.7 - - - +
74U ASN 3.2 0.8 - - - -
75U SER* 1.4 78.8 - - - +
77U MET* 1.4 56.6 + - - +
78U MET 3.0 8.3 + - - +
82U ASN* 5.4 0.2 - - - +
89U THR* 3.7 15.3 - - + -
92U ILE* 5.8 3.6 - - + -
93U VAL* 5.2 9.4 - - + -
155U CYS* 3.8 29.6 - - - +
158U ALA* 4.6 0.7 - - + -
159U ARG* 3.3 40.3 + - + -
169U ILE* 3.8 28.7 - - + -
173U LEU* 4.0 31.4 - - + -
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Residues in contact with MET 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530A U 3.5 11.7 - - - +
1669A G 3.6 26.7 - - - +
1670A A 3.7 29.0 - - - +
73U THR 4.3 4.3 - - - +
74U ASN* 3.3 25.9 - - - +
75U SER 3.4 0.4 - - - -
76U MET* 1.4 73.8 - - - +
78U MET* 1.4 66.9 + - - +
82U ASN 3.3 19.1 - - - +
83U ASN* 3.2 15.1 + - - -
84U GLY* 3.9 11.4 - - - +
85U LYS 3.6 31.6 - - - +
86U LYS* 3.8 16.2 - - + -
89U THR* 4.0 6.5 - - - +
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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