Contacts of the strand formed by residues 90 - 99 (chain C) in PDB entry 1K4R
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 THR 90 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU* 2.8 46.7 + - + +
85C GLU* 4.9 0.3 - - - -
87C GLN* 3.1 19.2 + - + +
88C GLY 3.4 6.7 - - - +
89C GLY* 1.3 83.8 + - - +
91C VAL* 1.3 66.9 + - - +
92C CYS* 4.1 7.3 + - - -
116C CYS* 4.8 0.2 - - - -
117C VAL 3.1 11.9 - - - +
118C LYS* 3.9 21.1 - - + -
119C ALA 4.3 0.2 - - - +
238C ALA* 5.7 0.7 - - - +
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Residues in contact with VAL 91 (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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90C THR* 1.3 77.1 - - - +
92C CYS* 1.3 64.0 - - - +
116C CYS* 3.2 1.7 - - - -
117C VAL* 2.8 41.8 + - + +
119C ALA* 3.9 11.2 - - + -
238C ALA* 3.6 33.2 - - + +
239C GLU* 3.9 33.9 - - + +
242C VAL* 4.5 9.6 - - + -
244C PHE* 3.7 23.1 - - + -
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Residues in contact with CYS 92 (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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85C GLU* 3.7 29.2 - - + +
90C THR* 4.1 11.0 + - - -
91C VAL* 1.3 80.0 - - - +
93C LYS* 1.3 62.5 + - - +
94C ARG* 4.4 1.6 - - + -
114C VAL* 4.5 3.8 - - + -
115C ALA 3.1 4.5 - - - +
116C CYS* 2.0 47.1 - - - -
244C PHE* 4.1 6.2 - - - -
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Residues in contact with LYS 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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92C CYS* 1.3 75.8 - - - +
94C ARG* 1.3 71.8 + - - +
95C ASP* 4.3 20.7 + - - +
114C VAL* 3.3 3.0 - - - -
115C ALA 2.9 30.3 + - - -
244C PHE* 3.6 49.7 + - + +
245C GLY 5.7 1.9 + - - +
252C MET* 3.4 13.5 - - + +
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Residues in contact with ARG 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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79C PRO* 3.7 14.1 - - - +
80C ALA* 2.8 33.7 + - - +
81C THR* 4.4 3.8 - - - +
85C GLU* 2.9 37.8 + - - +
92C CYS* 5.8 2.0 - - + -
93C LYS* 1.3 83.3 - - - +
95C ASP* 1.3 64.8 + - - +
112C SER* 3.5 17.6 + - - -
113C ILE 3.4 6.0 + - - +
114C VAL* 3.8 13.8 - - + +
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Residues in contact with ASP 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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93C LYS* 4.1 19.1 + - - -
94C ARG* 1.3 76.8 - - - +
96C GLN* 1.3 80.2 + - - +
112C SER* 3.9 4.0 + - - -
113C ILE* 2.8 36.7 + - + +
245C GLY 5.2 0.7 - - - +
246C ALA* 5.3 0.7 - - - -
247C PRO* 3.5 26.5 - - + +
252C MET* 4.3 11.5 - - - +
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Residues in contact with GLN 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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95C ASP* 1.3 90.8 + - - +
97C SER* 1.3 60.7 + - - +
110C LYS* 3.9 43.7 + - + +
111C GLY 3.2 14.5 - - - +
112C SER* 4.9 2.9 - - - -
113C ILE* 4.0 3.1 - - - -
247C PRO* 3.4 13.9 - - - +
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Residues in contact with SER 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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72C ALA* 5.3 0.5 - - - +
96C GLN* 1.3 75.2 - - - +
98C ASP* 1.3 63.9 + - - +
99C ARG* 3.5 11.1 + - - +
110C LYS* 3.4 5.6 - - - +
111C GLY 2.8 35.6 + - - -
112C SER 5.2 0.2 + - - -
113C ILE* 4.0 8.6 - - - +
247C PRO* 4.2 20.2 - - - -
249C ALA* 2.7 39.1 + - - -
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Residues in contact with ASP 98 (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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7B GLU* 4.6 27.2 - - + +
97C SER* 1.3 72.9 - - - +
99C ARG* 1.3 66.6 + - - +
103C ASN* 3.8 9.5 + - - -
109C GLY 3.7 5.7 - - - +
110C LYS* 2.8 35.0 + - - +
247C PRO 5.6 0.6 + - - -
248C HIS* 5.9 0.2 - - - +
249C ALA* 3.9 10.7 + - - +
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Residues in contact with ARG 99 (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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72C ALA* 3.8 22.4 + - - +
73C ARG 3.6 24.0 + - - +
74C CYS* 3.9 4.0 - - - -
75C PRO* 3.8 8.3 - - + -
97C SER* 3.5 23.5 + - - +
98C ASP* 1.3 84.5 - - - +
100C GLY* 1.3 57.8 + - - +
103C ASN* 2.8 47.6 + - - +
105C CYS* 3.3 26.6 - - - -
107C LEU 4.0 0.9 - - - -
108C PHE* 3.3 4.9 - - - +
109C GLY 2.8 32.9 + - - +
111C GLY* 4.0 15.3 - - - -
249C ALA 3.8 5.6 - - - -
250C VAL* 3.6 19.7 - - - +
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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