Contacts of the strand formed by residues 129 - 135 (chain C) in PDB entry 5KKR
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 PHE 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.8 3.1 - - - -
57C LYS* 3.2 26.4 + - - -
115C LEU* 4.0 21.5 - - + -
116C GLN* 4.2 2.2 - - - -
118C LEU* 3.4 36.3 + - + -
119C HIS* 3.2 63.7 - + - -
122C ASN* 4.5 1.4 + - - -
127C VAL 3.2 6.7 + - - +
128C GLY* 1.3 76.7 - - - -
130C TYR* 1.3 67.0 + - - +
131C GLY* 3.5 34.3 - - - -
132C ALA* 5.2 2.2 - - + -
141C ILE* 4.7 8.3 - - + -
142C CYS 3.9 8.7 - - - +
143C MET* 3.9 13.5 - - + +
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Residues in contact with TYR 130 (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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53C PHE* 3.3 35.1 - + - -
56C GLN 4.8 8.3 - - - -
57C LYS* 3.9 22.0 - - + +
60C VAL* 6.0 4.5 - - + -
63C LEU* 4.9 5.6 - - + -
92C LEU* 3.5 24.7 - - + +
93C VAL 4.9 1.0 + - - -
94C MET* 3.6 40.7 - - + +
119C HIS* 3.3 26.3 - - - -
129C PHE* 1.3 75.4 - - - +
131C GLY* 1.3 59.6 + - - +
142C CYS* 3.0 32.0 + - - -
143C MET 3.3 28.3 - - - -
144C GLU* 3.6 8.8 - - - +
145C HIS 4.8 1.2 + - - -
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Residues in contact with GLY 131 (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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63C LEU* 3.6 16.4 - - - +
116C GLN* 5.3 2.7 - - - -
119C HIS* 5.1 1.8 - - - -
129C PHE* 3.5 20.0 - - - -
130C TYR* 1.3 82.1 - - - +
132C ALA* 1.3 62.8 + - - +
141C ILE* 4.0 2.4 - - - +
142C CYS* 3.7 22.7 + - - -
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Residues in contact with ALA 132 (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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63C LEU* 3.7 4.7 - - - +
112C ILE* 3.8 25.1 - - + +
115C LEU* 3.7 33.0 - - + -
116C GLN* 4.6 9.8 + - - +
129C PHE* 4.6 3.1 - - + -
131C GLY* 1.3 74.6 - - - +
133C PHE* 1.3 67.2 + - - +
140C SER 3.6 12.6 - - - +
141C ILE* 4.1 4.3 - - + -
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Residues in contact with PHE 133 (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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63C LEU* 3.7 37.0 - - + +
64C LYS 4.7 0.4 - - - -
65C ASP* 4.0 17.5 - - + -
68C PHE* 3.5 33.0 - + - -
96C ARG* 3.7 27.8 - - + -
112C ILE* 4.2 9.2 - - - +
132C ALA* 1.3 77.2 - - - +
134C TYR* 1.3 81.9 + - - +
135C SER* 4.1 5.8 - - - -
139C ILE* 3.3 25.1 - - - +
140C SER* 3.4 35.6 + - - -
142C CYS* 5.3 3.1 - - - -
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Residues in contact with TYR 134 (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 ASP* 5.4 1.9 - - - +
101C LEU 3.4 19.7 + - - -
102C GLU* 5.1 0.3 - - - -
103C ILE* 3.8 28.9 + - + +
108C ARG* 3.2 59.6 + - + +
112C ILE* 5.8 3.6 - - + -
133C PHE* 1.3 87.1 - - - +
135C SER* 1.3 74.9 + - - +
136C ASP 3.2 27.4 + - - -
137C GLY* 3.6 12.1 - - - -
138C GLU 4.1 4.3 - - - -
139C ILE* 3.7 24.5 - - + -
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Residues in contact with SER 135 (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 ASP* 2.9 38.1 + - - -
96C ARG* 4.1 11.9 + - - -
133C PHE* 4.1 4.9 - - - -
134C TYR* 1.3 76.1 - - - +
136C ASP* 1.3 64.3 + - - +
137C GLY 2.5 18.9 + - - -
138C GLU* 2.9 38.5 + - - +
140C SER* 4.4 1.1 - - - -
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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