Contacts of the strand formed by residues 99 - 104 (chain E) in PDB entry 3EGC
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 SER 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E ASN 2.8 11.3 + - - -
69E VAL* 4.2 4.5 - - - -
70E VAL* 2.9 27.0 + - - +
97E GLY 4.1 0.6 + - - -
98E TYR* 1.3 75.0 - - - +
100E VAL* 1.3 65.7 + - - +
101E LEU 4.3 0.2 - - - -
101F LEU* 3.7 19.6 - - - +
118F GLN* 3.7 20.5 + - - +
119F PHE* 4.5 3.8 - - - -
122F ARG* 3.1 33.1 + - - +
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Residues in contact with VAL 100 (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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70E VAL* 3.6 5.4 - - + +
71E GLY 5.3 0.2 - - - -
72E LEU* 3.8 35.7 - - + -
89E VAL* 4.5 1.8 - - + -
90E GLU* 4.4 17.3 - - + -
93E ALA* 3.6 27.4 - - + -
98E TYR 4.6 0.7 - - - +
99E SER* 1.3 80.9 - - - +
101E LEU* 1.3 64.0 + - - +
102E LEU* 4.8 0.7 - - - +
308E MET* 4.3 12.1 - - + -
101F LEU* 3.3 5.8 - - - +
102F LEU* 2.7 56.8 + - + +
119F PHE* 5.9 0.6 - - - -
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Residues in contact with LEU 101 (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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69E VAL* 3.8 13.9 - - + -
70E VAL 3.0 12.0 + - - +
71E GLY* 4.4 0.4 - - - -
72E LEU* 2.7 34.1 + - - +
99E SER 4.3 0.2 - - - -
100E VAL* 1.3 72.8 - - - +
102E LEU* 1.3 57.7 + - - +
119E PHE* 3.6 24.3 - - + -
122E ARG* 4.0 23.6 - - + -
124E VAL* 3.7 26.2 - - + -
69F VAL* 4.5 4.7 - - + -
99F SER* 3.7 26.2 - - - -
100F VAL 3.4 17.9 - - - +
101F LEU* 3.9 15.7 - - + +
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Residues in contact with LEU 102 (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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72E LEU* 3.5 26.9 - - + +
74E VAL* 4.9 2.2 - - + -
77E ILE* 4.2 28.7 - - + -
100E VAL* 5.2 1.3 - - + -
101E LEU* 1.3 74.7 - - - +
103E ALA* 1.3 78.6 + - - +
104E ASN* 5.7 0.9 - - + -
119E PHE* 3.7 6.3 - - - -
72F LEU* 5.2 1.6 - - + -
77F ILE* 5.8 0.7 - - + -
86F ALA* 4.7 20.4 - - + -
90F GLU* 3.6 24.5 - - + +
100F VAL* 2.8 34.0 + - + +
102F LEU* 4.3 32.5 - - + -
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Residues in contact with ALA 103 (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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72E LEU 3.0 7.0 + - - +
73E ILE* 3.6 8.0 - - + -
74E VAL* 3.1 24.0 + - - +
102E LEU* 1.3 83.4 - - - +
104E ASN* 1.3 59.4 + - - +
115E ALA* 3.8 23.3 - - + -
118E GLN* 5.5 2.5 - - - +
119E PHE* 3.5 23.3 - - + -
90F GLU* 3.0 12.3 - - - +
94F ARG* 4.8 3.6 - - - +
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Residues in contact with ASN 104 (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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74E VAL* 3.5 4.1 - - - +
76E ASP* 3.4 12.6 + - - +
77E ILE* 2.9 43.7 + - + +
78E GLU* 4.6 3.6 + - - -
102E LEU* 5.7 1.6 - - + -
103E ALA* 1.3 73.7 - - - +
105E THR* 1.3 60.6 + - - +
106E ALA* 3.7 12.7 + - - +
111E ARG* 2.9 22.8 + - - +
87F SER* 3.3 24.4 + - - +
90F GLU* 2.8 25.3 + - + +
94F ARG* 2.9 11.8 + - - -
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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