Contacts of the helix formed by residues 66 - 77 (chain A) in PDB entry 6RKU
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LYS 3.8 0.6 + - - -
65A LYS* 1.3 70.7 - - - +
67A ALA* 1.3 65.9 + - - +
69A VAL* 3.3 2.8 + - - +
70A VAL* 2.9 31.3 + - - +
86A TYR* 4.4 15.2 - - - -
89A ILE* 5.8 2.7 - - - +
120A MET* 3.6 14.9 + - - -
121A ARG 6.3 0.2 - - - -
123A THR* 2.5 37.5 + - - -
125A ILE* 4.2 26.6 - - - +
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Residues in contact with ALA 67 (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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65A LYS* 3.2 7.9 - - + +
66A SER* 1.3 78.1 - - - +
68A ARG* 1.3 64.4 + - - +
70A VAL* 4.0 4.6 - - - +
71A GLY* 2.9 23.2 + - - -
120A MET* 3.8 15.3 + - - +
121A ARG* 5.7 1.6 - - - -
71C GLY* 4.1 18.8 - - - +
74C ILE* 4.2 26.9 - - + -
75C GLY 4.9 2.2 - - - +
101G JHN 4.4 13.7 - - + +
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Residues in contact with ARG 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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55A LEU* 4.8 26.1 - - + +
64A LYS* 4.9 20.7 - - + +
65A LYS* 3.5 19.8 + - + +
66A SER 3.3 0.6 - - - -
67A ALA* 1.3 77.9 - - - +
69A VAL* 1.3 59.8 + - + +
71A GLY* 3.8 0.5 - - - -
72A ASP* 2.9 31.2 + - - +
71C GLY 4.2 10.5 - - - +
72C ASP* 3.1 28.2 + - - +
75C GLY* 4.2 24.2 - - - -
76C LYS* 3.3 29.4 - - - +
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Residues in contact with VAL 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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48A VAL* 5.0 0.9 - - + -
51A ALA* 5.6 1.3 - - + -
52A MET* 4.0 38.6 - - + +
55A LEU* 4.8 15.7 - - + -
57A ASN* 5.3 9.6 - - + +
64A LYS* 5.5 4.7 - - + -
65A LYS 4.3 8.5 - - - +
66A SER 3.3 6.9 + - - +
68A ARG* 1.3 77.7 - - + +
70A VAL* 1.3 64.8 + - + +
72A ASP* 3.3 5.6 + - - +
73A VAL* 2.9 40.6 + - + +
89A ILE* 4.7 8.7 - - + -
125A ILE* 4.1 22.9 - - + -
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Residues in contact with VAL 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* 2.9 25.1 + - - +
67A ALA* 4.0 4.5 - - - +
69A VAL* 1.3 77.3 - - + +
71A GLY* 1.3 62.4 + - - +
73A VAL* 3.8 4.4 - - - +
74A ILE* 2.9 48.8 + - + +
82A ASP* 4.5 15.9 - - + +
85A VAL* 4.9 8.5 - - + +
86A TYR* 4.4 19.5 - - + -
89A ILE* 4.1 23.1 - - + -
120A MET* 4.6 15.7 - - + -
101G JHN 4.7 4.9 - - - -
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Residues in contact with GLY 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 ALA 2.9 17.4 + - - -
68A ARG 3.9 0.4 - - - -
70A VAL* 1.3 76.8 - - - +
72A ASP* 1.3 58.5 + - - +
74A ILE* 3.4 3.4 + - - +
75A GLY* 2.9 26.0 + - - -
67C ALA* 4.1 28.2 - - - +
68C ARG* 4.3 5.9 - - - +
71C GLY* 5.1 1.8 - - - -
101G JHN 4.1 11.2 - - - -
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Residues in contact with ASP 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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51A ALA* 4.0 21.4 - - + +
55A LEU* 5.2 14.5 - - + +
68A ARG 2.9 19.1 + - - +
69A VAL* 3.7 5.6 - - - +
71A GLY* 1.3 75.8 - - - +
73A VAL* 1.3 62.4 + - + +
75A GLY* 3.2 0.9 + - - -
76A LYS* 3.0 49.6 + - - +
77A TYR* 4.7 0.3 - - - -
68C ARG* 3.1 30.2 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 6.5 0.2 - - + -
47A ARG* 4.8 4.0 - - + +
48A VAL* 4.4 25.4 - - + +
51A ALA* 3.8 27.8 - - + -
69A VAL* 2.9 30.9 + - + +
70A VAL* 3.8 5.2 - - - +
72A ASP* 1.3 75.5 - - - +
74A ILE* 1.3 63.4 + - - +
77A TYR* 3.2 11.2 + - + +
78A HIS* 3.0 46.8 + - + +
85A VAL* 4.4 20.4 - - + -
89A ILE* 6.1 0.4 - - + -
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Residues in contact with ILE 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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70A VAL* 2.9 34.7 + - + +
71A GLY 3.8 3.4 - - - +
73A VAL* 1.3 78.1 - - + +
75A GLY* 1.3 62.0 + - - +
78A HIS 3.6 18.3 + - - +
79A PRO* 4.2 13.7 - - + +
81A GLY 3.2 32.1 - - - +
82A ASP* 3.6 22.9 - - + -
85A VAL* 5.0 6.3 - - + -
149A TYR* 5.8 0.5 - - - -
65C LYS* 5.3 4.2 + - - +
67C ALA* 4.2 14.8 - - + -
121C ARG* 5.0 16.4 - - + +
101G JHN 4.5 14.1 - - + -
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Residues in contact with GLY 75 (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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71A GLY 2.9 17.6 + - - -
72A ASP 3.2 1.3 + - - -
74A ILE* 1.3 80.3 - - - +
76A LYS* 1.3 61.6 + - - +
149A TYR* 3.7 18.5 + - - -
65C LYS* 4.3 20.6 + - - +
67C ALA* 5.1 2.0 - - - -
68C ARG* 4.2 18.7 - - - -
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Residues in contact with LYS 76 (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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51A ALA* 6.2 0.4 - - - +
54A VAL* 4.5 17.8 - - - +
72A ASP* 3.0 40.3 + - - +
75A GLY* 1.3 78.2 - - - +
77A TYR* 1.3 102.4 + - + +
148A ASN* 4.0 13.2 + - - +
149A TYR* 3.8 16.9 - - - -
153A GLU* 5.3 15.0 - - + +
68C ARG* 3.3 26.5 - - - +
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Residues in contact with TYR 77 (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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47A ARG* 3.0 43.5 + - + -
50A TYR* 3.5 29.3 + + - -
51A ALA* 4.6 21.8 - - + -
54A VAL* 4.8 5.5 - - + +
72A ASP 4.7 3.6 - - - -
73A VAL* 3.2 8.5 + - + +
75A GLY 3.8 0.6 - - - -
76A LYS* 1.3 124.8 + - + +
78A HIS* 1.3 61.5 + - + +
79A PRO* 3.3 10.4 - - - +
148A ASN* 5.4 3.3 - - - +
149A TYR* 4.7 5.1 + - - +
153A GLU* 4.4 20.2 + - + -
154A LYS 4.0 8.9 + - - -
155A ILE* 3.5 36.1 - - + -
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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