Contacts of the strand formed by residues 114 - 120 (chain C) in PDB entry 6EKK
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 CYS 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C HIS 3.1 18.5 + - - +
83C GLY* 3.1 2.3 - - - -
84C VAL 2.7 30.3 + - - -
112C ASP 3.7 4.0 + - - -
113C VAL* 1.3 76.5 - - - +
115C ARG* 1.3 55.9 + - - +
164C ILE* 4.0 17.3 - - + -
167C LEU* 3.6 38.4 - - + -
168C VAL* 3.9 6.5 - - - +
171C ALA* 3.8 18.8 - - - -
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Residues in contact with ARG 115 (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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84C VAL* 3.3 18.8 - - + +
86C VAL* 4.7 1.6 - - + -
103C LEU* 3.9 25.6 - - + -
106C ILE* 3.6 29.5 - - + +
107C ASN* 4.2 16.6 + - - +
110C CYS 4.0 0.2 + - - -
111C ASP* 2.6 50.7 + - - +
113C VAL* 2.7 24.4 + - + +
114C CYS* 1.3 75.5 - - - +
116C ILE* 1.3 68.1 + - - +
142C MET* 4.9 4.9 + - - +
144C ILE* 3.6 37.4 - - + +
145C GLN 4.8 1.0 + - - -
164C ILE* 4.2 1.1 - - - +
167C LEU* 4.3 6.2 - - - +
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Residues in contact with ILE 116 (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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84C VAL 3.2 8.8 + - - +
85C ILE* 4.4 4.7 - - + -
86C VAL* 3.0 32.1 + - - +
115C ARG* 1.3 79.1 - - - +
117C LEU* 1.3 60.8 + - - +
118C VAL* 4.1 7.4 - - + -
144C ILE* 4.6 5.6 - - - -
145C GLN* 3.8 14.6 - - + +
147C PHE* 4.1 9.9 - - + -
160C MET* 3.4 52.7 - - + +
163C CYS* 4.0 12.3 - - - -
164C ILE* 3.9 18.1 - - + +
167C LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 117 (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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86C VAL* 3.5 13.5 - - + +
88C TYR* 3.8 24.7 - - + -
96C PHE* 4.4 5.6 - - + -
99C VAL* 3.9 14.4 - - + -
103C LEU* 3.8 19.1 - - + -
116C ILE* 1.3 72.0 - - - +
118C VAL* 1.3 57.6 + - - +
135C ALA* 3.9 18.2 - - + +
138C PHE* 4.2 17.9 - - + -
139C ALA* 4.4 6.7 - - + -
144C ILE* 3.8 13.6 - - + +
145C GLN 2.9 14.5 + - - +
146C LEU* 3.3 22.6 - - + -
147C PHE* 2.8 32.6 + - - +
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Residues in contact with VAL 118 (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 LEU* 4.5 9.2 - - + -
85C ILE* 3.8 20.6 - - + -
86C VAL 2.8 13.0 + - - +
87C VAL* 3.3 15.6 - - + -
88C TYR* 2.9 33.6 + - - +
116C ILE* 4.1 7.4 - - + -
117C LEU* 1.3 79.3 - - - +
119C GLY* 1.3 61.1 + - - +
120C ASN 4.3 1.3 - - - +
147C PHE* 3.1 11.0 - - + +
149C THR* 3.6 28.5 - - + +
160C MET* 3.5 26.5 - - + -
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Residues in contact with GLY 119 (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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88C TYR* 3.3 36.1 + - - -
90C VAL* 3.5 10.5 - - - +
118C VAL* 1.3 69.6 - - - +
120C ASN* 1.3 64.3 + - - -
122C ASN* 4.1 0.7 - - - +
146C LEU* 4.2 1.2 - - - +
147C PHE 2.9 11.5 + - - -
148C GLU* 3.3 7.0 - - - +
149C THR* 2.8 24.6 + - - +
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Residues in contact with ASN 120 (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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19C VAL 2.9 27.6 + - - +
20C GLY* 3.6 9.5 + - - -
24C LEU* 4.1 7.8 - - + +
87C VAL* 4.0 11.7 - - + -
88C TYR 2.8 13.7 + - - +
89C ASP* 3.6 0.5 - - - -
90C VAL* 2.9 24.9 + - - +
118C VAL* 3.7 1.0 + - + -
119C GLY* 1.3 74.7 - - - +
121C LYS* 1.3 77.6 + - - +
122C ASN 3.3 0.8 + - - -
149C THR* 2.9 24.4 + - - +
151C ALA* 3.0 22.0 + - - +
204C GDP 3.1 28.5 + - - -
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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