Contacts of the strand formed by residues 68 - 75 (chain I) in PDB entry 3E8E
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 HIS 68 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ILE* 3.7 30.6 - - + +
59I LEU* 4.0 10.4 - - + +
60I VAL 3.4 3.1 + - - +
61I LYS* 4.0 18.4 + - + +
66I GLY 4.0 9.6 + - - -
67I ASN* 1.3 72.9 - - - +
69I TYR* 1.3 72.7 + - - +
122I TYR* 4.2 10.7 + - + +
321I PRO* 3.9 30.0 - - + +
322I GLY* 3.6 34.3 + - - -
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Residues in contact with TYR 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I PHE* 4.4 4.7 - + - -
59I LEU* 3.4 6.2 - - - +
60I VAL* 2.8 40.1 + - + +
62I HIS* 3.6 24.7 + + + -
65I THR* 4.9 0.2 + - - -
67I ASN* 3.2 46.7 + - + -
68I HIS* 1.3 77.2 - - - +
70I ALA* 1.3 56.5 + - - +
107I GLU* 3.6 34.4 + - + -
108I PHE* 4.3 17.2 - + - -
119I VAL* 3.5 23.1 - - + -
120I MET 3.4 17.3 - - - +
121I GLU* 4.7 3.1 - - - -
122I TYR* 3.7 9.4 - - - -
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LEU* 4.4 7.4 - - + -
57I VAL* 4.1 9.6 - - + -
58I MET 3.2 7.9 - - - +
59I LEU* 4.6 0.7 - - - +
69I TYR* 1.3 75.5 - - - +
71I MET* 1.3 60.3 + - - +
119I VAL* 3.4 4.5 - - - +
120I MET* 2.9 47.1 + - + +
121I GLU 4.2 0.7 - - - +
122I TYR* 3.7 4.0 - - + +
351I G98 3.9 34.1 - - + +
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Residues in contact with MET 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LEU* 4.0 15.3 - - + -
43I PHE* 3.6 45.3 - - + -
45I ARG* 5.2 2.9 - - - -
56I ARG 3.6 0.5 - - - +
57I VAL* 3.4 2.1 - - - -
58I MET* 2.7 41.9 + - + +
60I VAL* 3.8 19.3 - - + -
70I ALA* 1.3 74.2 - - - +
72I LYS* 1.3 65.1 + - - +
73I ILE* 3.6 23.8 + - + +
110I PHE* 4.5 2.5 - - + -
117I TYR* 3.8 23.6 - - + -
118I MET 3.3 10.1 - - - +
119I VAL* 3.9 17.0 - - + -
120I MET* 4.0 0.9 - - - -
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Residues in contact with LYS 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ARG 3.5 4.5 - - - +
57I VAL* 4.0 14.1 - - + +
71I MET* 1.3 71.8 - - - +
73I ILE* 1.3 61.6 + - - +
74I LEU* 3.6 17.9 - - + +
91I GLU* 2.7 35.0 + - - +
116I LEU 3.6 1.2 - - - +
117I TYR* 3.4 6.1 - - - -
118I MET* 2.8 49.4 + - + +
120I MET* 3.5 12.2 - - + +
184I ASP* 3.2 21.0 + - - -
186I GLY* 4.7 1.2 - - - -
351I G98 3.3 61.3 + - + +
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Residues in contact with ILE 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ARG* 4.8 3.6 - - - +
55I GLY* 3.1 4.3 - - - -
56I ARG* 2.7 41.8 + - + +
58I MET* 4.2 21.5 - - + -
71I MET* 3.8 24.9 - - + +
72I LYS* 1.3 76.7 - - - +
74I LEU* 1.3 63.9 + - - +
115I ASN* 3.8 19.5 - - + +
116I LEU 3.4 2.7 - - - -
117I TYR* 3.6 29.8 - - + -
335I ILE* 3.2 41.3 - - + -
351I G98 5.1 0.2 - - - -
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I PHE* 3.5 28.0 - - + +
72I LYS* 3.6 36.6 - - + +
73I ILE* 1.3 79.0 - - - +
75I ASP* 1.3 64.8 + - - +
76I LYS 3.2 1.7 + - - -
79I VAL* 4.0 8.3 - - + -
88I THR* 3.4 33.7 - - + -
91I GLU* 4.5 10.5 - - - +
115I ASN* 3.4 5.5 - - - -
116I LEU* 2.9 54.0 + - + +
117I TYR 5.2 0.2 - - - +
118I MET* 4.1 13.5 - - + -
351I G98 5.0 2.9 - - + -
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Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I PHE 3.0 13.0 + - - +
55I GLY* 4.4 2.8 - - - +
73I ILE* 4.2 1.8 + - - +
74I LEU* 1.3 68.7 - - - +
76I LYS* 1.3 59.5 + - - +
77I GLN* 3.2 24.2 + - - +
78I LYS* 3.2 36.9 + - + +
79I VAL* 2.9 29.9 + - - +
114I SER* 4.1 6.2 - - - +
115I ASN* 3.7 14.2 + - - +
336I ARG* 5.8 3.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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