Contacts of the strand formed by residues 91 - 97 (chain C) in PDB entry 3E20
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 VAL 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LEU 3.5 2.7 - - - +
35C ILE* 3.9 26.7 - - + -
90C LEU* 1.3 81.2 - - - +
92C ILE* 1.3 67.0 + - - +
93C TYR* 3.4 30.5 - - + -
109C ILE 3.8 0.3 - - - +
110C ASP* 3.0 5.7 - - - -
111C PHE* 2.9 55.0 + - + +
113C PRO* 3.5 28.0 - - + -
116C PRO* 4.8 2.0 - - + -
133C LEU* 4.5 9.2 - - + -
136C LEU* 5.8 0.2 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 3.8 1.3 - - + +
33C THR* 3.6 2.1 - - - -
34C LEU* 2.9 52.8 + - + +
75C THR* 4.1 20.2 - - + -
78C ARG* 4.1 19.1 - - + -
79C LEU* 3.9 24.0 - - + -
82C TYR* 5.3 1.6 - - + -
90C LEU* 3.6 21.8 - - + -
91C VAL* 1.3 81.7 - - - +
93C TYR* 1.3 69.2 + - - +
94C CYS* 4.3 1.3 - - + -
108C ASN* 3.7 17.7 - - - +
109C ILE 3.1 8.7 - - - +
110C ASP* 3.6 12.6 - - + -
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Residues in contact with TYR 93 (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 LEU* 5.5 0.2 - - + -
21C LEU* 3.6 23.6 - - + -
32C ILE 3.5 1.3 - - - -
33C THR* 3.7 19.5 - - + -
35C ILE* 4.4 9.5 - - + +
91C VAL* 3.4 24.5 - - + -
92C ILE* 1.3 74.3 - - - +
94C CYS* 1.3 61.7 + - - +
107C LEU* 3.7 2.2 - - - +
108C ASN* 3.3 3.3 + - - -
109C ILE* 2.8 43.0 + - + +
111C PHE* 4.8 9.0 - + - -
128C PHE* 3.2 42.6 - + + -
129C HIS 2.8 30.2 + - - -
130C THR* 3.6 1.1 - - + -
133C LEU* 3.2 37.9 + - + +
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Residues in contact with CYS 94 (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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31C MET* 3.4 4.2 - - - -
32C ILE* 2.7 41.4 + - + +
71C ALA* 4.0 4.5 - - - -
74C SER* 3.8 24.2 - - - -
75C THR* 3.4 27.6 - - - +
92C ILE* 4.3 4.0 - - + -
93C TYR* 1.3 76.4 - - - +
95C GLY* 1.3 68.5 + - - +
106C LYS* 5.2 2.7 - - - -
107C LEU 3.1 7.4 - - - -
108C ASN* 3.5 28.7 - - - +
128C PHE* 3.5 8.5 - - - -
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Residues in contact with GLY 95 (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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30C SER 3.7 15.7 - - - -
31C MET* 4.7 3.1 - - - -
71C ALA* 4.6 8.1 - - - -
94C CYS* 1.3 83.4 - - - +
96C GLU* 1.3 56.5 + - - -
97C VAL* 4.0 0.3 + - - +
106C LYS* 4.2 6.3 - - - -
107C LEU* 2.7 39.8 + - - +
128C PHE* 4.7 5.4 - - - -
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Residues in contact with GLU 96 (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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26C GLY* 4.3 5.7 - - - -
27C ASN* 5.3 0.5 + - - +
30C SER* 4.7 7.4 + - - +
31C MET* 4.2 11.2 - - - +
67C SER* 4.4 18.7 + - - +
70C SER* 6.1 1.0 - - - -
95C GLY* 1.3 73.0 - - - -
97C VAL* 1.3 59.9 + - - +
104C THR* 4.1 22.7 + - + +
105C ARG 3.6 5.4 - - - -
106C LYS* 3.5 39.7 - - + +
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Residues in contact with VAL 97 (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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24C CYS* 3.3 42.8 - - + -
25C HIS 3.3 22.9 - - - +
26C GLY* 4.5 1.8 - - - -
31C MET* 4.7 5.6 - - + -
95C GLY 5.2 1.1 - - - +
96C GLU* 1.3 75.3 - - - +
98C ILE* 1.3 75.4 + - + +
99C MET* 3.5 19.5 - - + +
104C THR* 3.6 4.9 - - - -
105C ARG* 3.3 30.4 + - - +
107C LEU* 4.7 15.9 - - + -
128C PHE* 5.2 2.0 - - + -
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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