Contacts of the strand formed by residues 72 - 78 (chain C) in PDB entry 3E5X
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 GLU 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C ASP* 2.4 40.0 - - + +
65C ILE 3.1 13.5 - - - +
66C ILE* 4.0 14.7 - - + +
67C PHE* 5.8 0.2 - - - -
70C GLY 4.2 8.2 - - - +
71C SER* 1.3 76.7 - - - +
73C LYS* 1.3 80.6 + - - +
95C TYR* 3.3 26.8 - - - -
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ASP* 3.2 7.4 - - - -
65C ILE* 2.9 34.7 + - + +
67C PHE* 4.9 3.1 - - + -
71C SER* 6.3 1.1 - - - -
72C GLU* 1.3 84.3 + - - +
74C LEU* 1.3 66.5 + - - +
190C HIS* 6.2 0.8 - - - -
142D ALA* 3.9 28.3 - - + +
145D ASN* 3.5 31.3 + - + +
146D THR* 3.3 31.1 - - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO* 5.0 11.9 - - + -
62C LYS* 3.7 25.3 - - + +
64C ASP* 3.3 20.3 + - - +
73C LYS* 1.3 76.9 - - - +
75C LEU* 1.3 70.1 + - - +
76C TYR* 3.7 25.1 - - - +
77C TYR* 3.5 21.1 - - + -
137C TYR* 5.7 0.3 - - - -
185C GLU* 3.5 58.3 - - + +
186C ILE* 5.2 3.1 - - + +
141D VAL* 5.8 3.3 - - - +
142D ALA* 5.3 1.0 - - - +
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO* 3.4 15.2 - - - +
63C LEU* 2.9 36.6 + - + +
65C ILE* 3.8 30.5 - - + +
73C LYS 3.5 0.6 + - - -
74C LEU* 1.3 84.8 - - - +
76C TYR* 1.3 61.7 + - + +
92C ASN* 6.0 0.2 - - - +
94C ILE* 3.9 20.2 - - + -
137C TYR* 2.7 32.1 + - + +
502C 3C4 4.3 11.9 - - + -
138D ALA* 3.7 44.0 - - + +
141D VAL* 6.0 1.6 - - + -
142D ALA* 4.4 3.6 - - + +
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO 3.3 14.4 - - - +
19C PHE* 3.7 20.6 - + + -
61C ILE* 5.9 0.2 - - + -
62C LYS 3.8 0.2 - - - -
63C LEU* 2.8 44.4 + - + +
74C LEU* 3.7 13.0 - - - +
75C LEU* 1.3 84.2 - - + +
77C TYR* 1.3 73.5 + - - +
78C ALA* 3.9 17.7 - - + -
82C SER* 6.0 0.9 - - - -
83C LEU 3.7 3.5 + - - -
84C ILE* 3.5 23.0 - - + +
133C LYS* 4.2 14.6 - - + -
137C TYR* 3.3 21.3 - + - +
502C 3C4 2.5 48.8 + + - -
134D VAL* 6.2 0.2 - - + -
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Residues in contact with TYR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 6.3 0.7 - - + -
16C PRO* 3.0 10.9 + - + +
17C ASP* 3.2 27.6 - - + +
18C ASN* 3.0 21.1 + - - -
19C PHE* 4.8 0.9 + - - -
60C LYS* 4.2 12.3 - - - +
61C ILE 3.4 3.6 - - - +
62C LYS* 3.4 38.2 + - + +
74C LEU* 3.5 19.7 - - + -
76C TYR* 1.3 82.4 - - - +
78C ALA* 1.3 61.7 + - - +
99C MET* 3.5 38.0 - - + +
182C SER* 5.3 3.7 + - - -
185C GLU* 2.6 32.0 + - - -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASP* 5.1 0.7 - - - -
18C ASN* 3.5 2.5 - - - +
56C LEU* 3.3 11.7 - - + +
60C LYS* 3.3 8.4 - - - +
61C ILE* 2.8 40.6 + - + +
76C TYR* 3.9 19.7 - - + -
77C TYR* 1.3 77.1 - - - +
79C GLY* 1.3 58.6 + - - +
82C SER* 3.6 23.1 - - - -
84C ILE* 5.5 5.8 - - + -
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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