Contacts of the strand formed by residues 64 - 71 (chain E) in PDB entry 4QAE
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 TYR 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E PHE* 3.7 5.0 - + - -
24E ASP* 2.5 45.0 + - + -
27E PHE* 3.5 15.3 - + - +
28E HIS* 4.2 5.6 - - - -
56E TYR* 3.8 36.1 - + + -
57E GLU 3.2 5.6 - - - +
58E LEU* 3.8 33.7 - - + -
62E LYS 5.5 0.2 - - - -
63E SER* 1.3 74.9 - - - +
65E ASN* 1.3 63.3 + - - +
66E VAL* 3.8 17.3 + - + +
82E THR* 3.4 6.4 - - - +
83E PHE* 2.9 38.3 + - + +
92E PHE* 3.5 42.8 - + - -
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Residues in contact with ASN 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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55E ILE 3.6 1.9 - - - +
57E GLU* 2.9 44.3 + - + +
59E GLU* 3.1 30.4 + - - +
63E SER* 4.1 2.8 + - - -
64E TYR* 1.3 71.8 - - - +
66E VAL* 1.3 62.2 + - - +
67E THR* 5.2 1.1 - - - -
81E GLN 3.9 4.0 - - - +
82E THR* 3.9 18.9 + - - +
1U ASP 3.0 28.3 + - - +
2U THR 4.2 0.4 - - - -
3U HIS* 3.8 34.9 + - + +
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Residues in contact with VAL 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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54E THR* 3.3 32.3 - - + -
55E ILE 3.2 4.9 - - - +
56E TYR* 4.3 7.6 - - + -
64E TYR* 3.9 14.6 - - + +
65E ASN* 1.3 76.6 - - - +
67E THR* 1.3 64.1 + - - +
68E ILE* 4.2 11.0 - - + -
79E LEU 3.9 0.2 - - - +
80E PHE* 3.3 9.0 - - - +
81E GLN* 2.9 41.2 + - + +
83E PHE* 3.7 45.5 - - + -
3U HIS* 5.5 0.8 + - - -
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Residues in contact with THR 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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53E ALA 3.8 0.3 - - - +
54E THR* 3.4 2.9 - - - -
55E ILE* 2.8 53.8 + - + +
57E GLU* 4.8 3.1 + - - -
65E ASN 4.1 1.2 + - - -
66E VAL* 1.3 75.3 - - - +
68E ILE* 1.3 69.6 + - - +
69E VAL* 4.0 13.8 + - + -
78E TYR* 4.6 7.6 - - + -
79E LEU 3.5 3.1 - - - +
80E PHE* 3.7 19.9 - - + -
3U HIS* 3.1 29.9 + - + -
23U CYS* 6.2 1.3 - - + -
25U THR* 4.5 12.5 - - + +
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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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52E TRP* 3.7 30.1 - - + -
53E ALA 3.4 2.9 - - - +
54E THR* 4.1 18.6 - - + +
66E VAL* 4.2 4.5 - - + -
67E THR* 1.3 76.3 - - - +
69E VAL* 1.3 62.4 + - - +
70E MET* 3.9 15.5 - - + -
77E GLU 3.4 1.6 - - - +
78E TYR* 3.2 7.1 - - - +
79E LEU* 2.6 51.2 + - + +
81E GLN* 3.4 32.3 - - + +
9T PHE* 3.7 38.1 - - + -
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Residues in contact with VAL 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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30E LYS* 5.9 1.6 - - - -
52E TRP* 3.2 7.1 - - - +
53E ALA* 2.9 35.3 + - + +
55E ILE* 3.8 28.7 - - + -
67E THR* 4.4 2.2 - - + -
68E ILE* 1.3 74.1 - - - +
70E MET* 1.3 64.2 + - - +
76E CYS* 4.9 0.4 - - + -
77E GLU 3.4 3.6 - - - +
78E TYR* 3.7 33.0 - - + -
175E CYS* 3.5 39.7 - - + +
176E ILE* 3.9 8.5 - - + +
25U THR* 4.2 4.7 - - - +
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Residues in contact with MET 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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49E MET* 6.2 2.2 - - + -
52E TRP* 4.0 20.4 - - + -
68E ILE* 3.9 14.4 - - + +
69E VAL* 1.3 78.9 - - - +
71E PRO* 1.3 68.4 - - + +
72E LEU* 3.5 12.6 + - + -
76E CYS* 3.7 1.6 - - - -
77E GLU* 2.8 51.8 + - + +
79E LEU* 4.6 8.5 - - + -
175E CYS* 4.6 4.0 - - - -
9T PHE* 4.1 20.6 - - - -
19T CYS* 3.3 42.2 - - + +
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Residues in contact with PRO 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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74D GLU* 4.9 0.2 - - - +
50E LYS* 4.0 20.7 + - + +
51E MET 3.2 27.6 - - - +
52E TRP* 4.1 5.2 - - + -
69E VAL 4.0 4.7 - - - +
70E MET* 1.3 87.5 - - + +
72E LEU* 1.3 67.4 + - - +
172E ILE* 3.5 24.7 - - + -
175E CYS* 3.8 21.1 - - + -
176E ILE* 4.6 3.6 - - + -
201E MPD 4.2 13.8 - - + +
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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