Contacts of the strand formed by residues 121 - 125 (chain C) in PDB entry 1EFA
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 GLY 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C LEU 3.9 0.8 + - - -
64C ILE 3.8 1.0 - - - -
65C GLY 2.8 25.5 + - - -
119C VAL* 3.2 4.9 + - - +
120C SER* 1.3 82.6 + - - +
122C LEU* 1.3 67.4 + - - +
143C VAL* 4.4 4.3 - - - -
144C PRO* 3.5 13.5 - - - -
304C LEU* 3.6 20.2 - - - -
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Residues in contact with LEU 122 (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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65C GLY* 3.5 3.8 - - - -
111C VAL* 3.4 38.1 - - + -
114C LEU* 3.6 27.1 - - + -
115C LEU* 4.1 9.0 - - + -
119C VAL* 3.3 23.1 - - + -
121C GLY* 1.3 84.6 - - - +
123C ILE* 1.3 63.4 + - - +
124C ILE* 3.9 19.7 - - + -
140C CYS* 3.6 15.0 - - - -
143C VAL* 4.9 2.5 - - + -
144C PRO 2.9 12.0 + - - +
145C ALA* 3.5 7.1 - - + -
146C LEU 3.0 23.1 + - - -
304C LEU* 3.3 10.5 - - - +
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Residues in contact with ILE 123 (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 ILE* 4.1 16.8 - - + -
65C GLY 3.0 10.1 + - - +
66C VAL* 3.3 9.1 - - + +
67C ALA 3.0 25.5 + - - +
83C ILE* 4.1 27.1 - - + -
122C LEU* 1.3 77.4 - - - +
124C ILE* 1.3 64.0 + - - +
125C ASN* 4.8 1.6 - - + +
146C LEU* 3.4 11.2 - - + +
148C LEU* 4.0 30.7 - - + -
300C SER* 3.9 32.1 - - - +
301C VAL* 4.3 3.4 - - - +
304C LEU* 3.8 17.0 - - + -
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Residues in contact with ILE 124 (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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67C ALA* 3.5 14.8 - - + +
107C CYS* 3.9 24.5 - - - -
111C VAL* 3.7 27.8 - - + -
122C LEU* 3.9 20.4 - - + -
123C ILE* 1.3 74.6 - - - +
125C ASN* 1.3 58.8 + - - +
126C TYR* 3.6 11.2 + - + +
128C LEU* 4.0 16.8 - - + -
136C VAL* 4.2 4.5 - - + -
140C CYS* 5.3 0.4 - - - -
145C ALA* 4.9 2.9 - - + -
146C LEU 2.8 12.3 + - - +
147C PHE* 3.5 31.7 - - + +
148C LEU 3.0 25.4 + - - -
149C ASP 4.1 0.7 + - - -
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Residues in contact with ASN 125 (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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66C VAL* 5.4 2.7 - - + -
67C ALA 2.7 13.5 + - - +
68C THR* 3.2 15.7 + - - +
69C SER* 3.1 26.6 + - - -
76C PRO* 4.0 13.5 - - - +
79C ILE* 3.8 26.3 - - + +
80C VAL* 5.9 0.7 - - + +
83C ILE* 6.1 0.2 - - + -
123C ILE* 3.7 4.6 + - + +
124C ILE* 1.3 70.7 - - - +
126C TYR* 1.3 58.6 + - - +
148C LEU* 4.1 24.0 - - + +
149C ASP* 4.1 5.3 + - - +
903C NPF 3.8 28.9 + - - -
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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