Contacts of the strand formed by residues 62 - 74 (chain E) in PDB entry 2Y6T
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 PHE 62 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E GLN* 3.5 49.4 - - + -
58E ASP 3.4 21.3 - - - -
59E GLU* 3.3 8.8 - - - +
60E SER* 3.1 5.9 + - - +
61E ARG* 1.3 100.7 - - + +
63E LYS* 1.3 67.5 + - - +
135E ARG* 5.1 0.9 - - - +
136E TYR* 3.3 44.6 + + + +
156E ILE* 5.0 11.4 - - + -
157E TRP 3.4 7.9 - - - -
158E GLU* 3.4 42.0 - - + -
157F TRP* 3.6 3.8 - - - -
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E PHE* 1.3 79.4 - - - +
64E VAL* 1.3 60.0 + - - +
65E GLU 4.2 0.2 - - - -
133E MET* 3.8 35.3 + - + +
134E GLN 3.7 15.4 + - - +
135E ARG* 5.0 4.7 - - - +
136E TYR* 4.3 6.6 - - - -
156E ILE* 3.5 4.9 - - - +
157E TRP* 2.8 34.8 + - + -
65F GLU* 4.4 11.0 + - - +
133F MET* 4.2 26.1 - - + +
157F TRP* 3.5 38.1 - - + -
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE* 5.1 1.3 - - + -
53E LEU* 4.7 9.9 - - + -
63E LYS* 1.3 73.4 - - - +
65E GLU* 1.3 62.2 + - - +
66E LEU* 3.8 6.6 + - + -
132E ALA 3.5 2.1 - - - +
133E MET* 3.7 3.7 - - - -
134E GLN* 2.8 58.7 + - + +
135E ARG 3.6 12.8 - - - +
136E TYR* 4.5 12.3 - - + -
142E ILE* 3.7 21.1 - - + -
154E TYR* 3.8 37.7 - - + -
155E ARG 3.5 3.1 - - - +
156E ILE* 4.7 1.8 - - + +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LYS 4.2 1.0 + - - -
64E VAL* 1.3 71.0 - - - +
66E LEU* 1.3 69.5 + - - +
67E LEU* 3.5 24.5 + - - +
132E ALA* 3.4 14.8 - - + +
133E MET* 3.7 16.3 - - - +
154E TYR* 3.1 6.0 - - - -
155E ARG* 2.7 48.9 + - + +
157E TRP* 3.2 39.9 + - + +
63F LYS* 4.4 11.3 + - - -
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE* 3.8 28.3 - - + -
64E VAL* 4.5 11.9 - - + -
65E GLU* 1.3 77.3 - - - +
67E LEU* 1.3 62.2 + - - +
68E ILE* 3.7 12.6 - - + -
85E LEU* 3.8 20.6 - - + -
98E LEU* 3.7 27.4 - - + -
128E LEU* 3.3 25.6 - - + +
131E ALA 4.2 4.3 - - - +
132E ALA* 3.0 11.4 + - - +
134E GLN* 4.0 18.4 - - + -
142E ILE* 4.3 12.3 - - + -
144E VAL* 4.7 7.0 - - + -
152E VAL* 4.9 2.9 - - + -
153E LYS 3.7 2.9 - - - +
154E TYR* 4.6 0.9 - - + -
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E GLU* 3.5 34.9 + - - +
66E LEU* 1.3 72.5 - - - +
68E ILE* 1.3 60.1 + - - +
123E PHE* 3.5 10.7 - - + -
125E THR* 4.1 24.0 - - + -
153E LYS* 2.6 41.5 + - + +
154E TYR 4.2 11.2 - - - -
155E ARG* 4.2 11.0 - - + +
163F ILE* 3.8 40.2 - - + -
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Residues in contact with ILE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 3.7 13.7 + - + -
67E LEU* 1.3 75.0 - - - +
69E GLY* 1.3 61.7 + - - +
85E LEU* 4.0 34.1 - - + -
100E MET* 4.5 11.2 - - + -
123E PHE* 4.5 0.2 - - - -
125E THR* 3.3 5.7 - - - +
126E ALA* 2.8 29.4 + - + +
128E LEU* 4.0 27.5 - - + +
144E VAL* 4.2 12.3 - - + -
146E VAL* 3.9 16.6 - - + -
150E VAL* 3.6 20.4 - - + -
151E GLU 3.6 7.4 - - - +
152E VAL* 4.2 16.8 - - + -
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Residues in contact with GLY 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ILE* 1.3 76.9 - - - +
70E LYS* 1.3 58.9 + - - -
81E LEU* 4.5 5.2 - - - -
123E PHE* 3.4 16.0 - - - -
124E VAL 3.1 14.1 - - - -
126E ALA* 4.4 2.5 - - - -
150E VAL* 3.4 11.6 - - - +
151E GLU* 2.8 39.0 + - - +
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Residues in contact with LYS 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E GLY* 1.3 74.9 - - - -
71E THR* 1.3 63.6 + - - +
72E LEU* 3.7 20.2 + - + -
81E LEU* 4.0 23.3 - - + +
103E ILE* 4.9 13.7 - - - +
123E PHE* 3.5 6.3 - - - -
124E VAL* 2.8 33.6 + - - +
149E GLY* 4.1 32.5 - - - +
150E VAL* 4.4 13.5 - - + -
151E GLU* 5.0 1.1 - - - +
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Residues in contact with THR 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LYS* 1.3 73.4 - - - +
72E LEU* 1.3 70.4 + - - +
73E ASN* 5.7 0.2 - - - +
121E VAL* 4.2 21.3 - - + -
122E LYS 3.8 9.9 - - - +
123E PHE* 3.6 12.6 - - + -
151E GLU* 3.1 23.3 + - - +
153E LYS* 5.1 0.5 + - - -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LYS* 3.7 23.7 + - + -
71E THR* 1.3 79.4 - - - +
73E ASN* 1.3 70.5 - - - +
74E VAL* 3.7 18.2 + - + -
79E HIS* 6.0 2.7 - - + -
81E LEU* 5.5 7.4 - - + -
106E PRO* 5.7 7.2 - - + -
120E GLN 3.7 0.3 - - - +
121E VAL* 3.6 1.4 - - - +
122E LYS* 2.8 36.6 + - - +
124E VAL* 4.1 22.2 - - + -
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Residues in contact with ASN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E THR* 5.7 0.2 - - - +
72E LEU* 1.3 81.1 - - - +
74E VAL* 1.3 62.5 + - - +
119E PRO* 3.9 25.2 - - + +
120E GLN 3.3 8.5 - - - +
121E VAL* 3.6 22.2 - - - +
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LEU* 4.0 22.7 - - + +
73E ASN* 1.3 75.6 - - - +
75E ASP* 1.3 71.7 + - - +
77E ASN 4.5 2.9 - - - +
79E HIS* 3.4 43.3 - - + +
119E PRO* 3.3 6.9 - - - +
120E GLN* 3.0 35.7 + - + +
122E LYS* 4.0 26.9 - - + -
124E VAL* 4.1 8.5 - - + -
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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