Contacts of the strand formed by residues 64 - 71 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F PHE* 3.7 3.9 - + - -
24F ASP* 2.5 40.7 + - + -
27F PHE* 3.5 18.2 - + - +
28F HIS* 4.2 6.1 - - - -
56F TYR* 3.8 33.9 - + + -
57F GLU 3.4 19.5 - - - +
58F LEU* 3.7 23.3 - - + -
63F SER* 1.3 74.8 - - - +
65F ASN* 1.3 62.0 + - - +
66F VAL* 3.7 17.6 + - + -
82F THR* 3.4 6.9 - - - +
83F PHE* 2.9 38.3 + - + +
92F PHE* 3.5 40.2 - + - -
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Residues in contact with ASN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE 3.5 2.1 - - - +
57F GLU* 3.0 43.0 + - - +
59F GLU* 3.3 23.8 + - - +
63F SER* 4.2 1.5 + - - -
64F TYR* 1.3 70.9 - - - +
66F VAL* 1.3 60.2 + - - +
67F THR* 5.2 0.2 + - - -
81F GLN 3.8 4.5 - - - +
82F THR* 3.7 18.5 + - - +
2S THR* 3.2 43.3 + - - +
3S HIS* 3.8 34.5 - - + +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR* 3.5 30.5 - - + -
55F ILE 3.2 4.5 - - - +
56F TYR* 4.2 9.0 - - + -
64F TYR* 3.9 15.9 - - + +
65F ASN* 1.3 77.0 - - - +
67F THR* 1.3 62.5 + - - +
68F ILE* 4.2 11.9 - - + -
80F PHE* 3.3 9.4 - - - +
81F GLN* 2.9 51.0 + - + +
83F PHE* 3.8 36.3 - - + -
3S HIS* 4.6 1.3 - - - -
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Residues in contact with THR 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ALA 3.8 0.7 - - - +
54F THR* 3.4 2.9 - - - -
55F ILE* 2.8 53.2 + - + +
57F GLU* 4.5 2.4 + - - -
65F ASN 4.2 0.7 + - - -
66F VAL* 1.3 69.5 - - - +
68F ILE* 1.3 66.3 + - - +
69F VAL* 4.0 17.7 + - + -
78F TYR* 4.5 10.1 - - + -
79F LEU 3.5 3.4 - - - +
80F PHE* 3.8 18.3 - - + -
3S HIS* 2.9 31.2 + - - -
23S CYS* 6.2 1.1 - - + -
24S LYS 5.9 2.7 - - - +
25S THR* 5.6 2.7 - - - +
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Residues in contact with ILE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TRP* 3.8 26.7 - - + -
53F ALA 3.5 2.2 - - - -
54F THR* 4.1 19.1 - - + +
66F VAL* 4.2 4.9 - - + -
67F THR* 1.3 75.5 - - - +
69F VAL* 1.3 62.6 + - - +
70F MET* 3.9 14.8 + - + -
77F GLU 3.4 1.2 - - - +
78F TYR* 3.2 7.6 - - - +
79F LEU* 2.7 48.9 + - + +
81F GLN* 3.2 34.1 - - + +
9U PHE* 3.8 37.7 - - + -
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Residues in contact with VAL 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TRP* 3.3 7.1 - - - +
53F ALA* 2.8 42.1 + - + +
55F ILE* 4.6 8.3 - - + -
67F THR* 4.1 14.4 - - + +
68F ILE* 1.3 75.2 - - - +
70F MET* 1.3 63.3 + - - +
76F CYS* 5.3 0.4 - - + -
77F GLU 3.5 3.1 - - - +
78F TYR* 3.8 28.9 - - + -
175F CYS* 3.6 37.2 - - + +
176F ILE* 3.9 5.1 - - + +
25S THR* 3.9 19.1 - - - +
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Residues in contact with MET 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLU 6.1 0.4 - - - +
49F MET* 6.4 0.9 - - + -
52F TRP* 3.6 22.9 - - + -
68F ILE* 3.9 22.2 - - + -
69F VAL* 1.3 79.6 - - - +
71F PRO* 1.3 69.2 - - + +
72F LEU* 3.4 12.6 + - + -
76F CYS* 3.8 1.9 - - - -
77F GLU* 2.9 49.2 + - + +
79F LEU* 4.6 8.5 - - + -
175F CYS* 4.6 3.4 - - - -
9U PHE* 4.2 11.2 - - - -
18U LYS* 6.6 0.2 - - + -
19U CYS* 3.0 40.8 - - + +
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Residues in contact with PRO 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 3.9 20.3 + - + +
51F MET 3.3 26.9 - - - +
52F TRP* 4.1 5.8 - - + -
69F VAL 4.2 1.6 - - - +
70F MET* 1.3 88.6 - - + +
72F LEU* 1.3 66.9 + - - +
172F ILE* 3.4 25.6 - - + -
175F CYS* 3.7 18.4 - - + -
176F ILE* 4.6 3.1 - - + -
203F MPD 3.6 18.4 + - - +
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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