Contacts of the strand formed by residues 213 - 219 (chain C) in PDB entry 1KWV
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 HIS 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ARG* 3.0 20.5 + - - +
119C MET* 2.9 27.3 + - - +
154C SER* 2.5 38.3 + - - +
156C PHE* 3.7 33.2 - + + +
197C THR* 3.7 25.1 - - + +
207C ILE* 4.0 16.1 - - + +
211C ALA* 3.9 19.6 - - + +
212C SER* 1.3 78.1 + - - +
214C THR* 1.3 65.8 + - - +
215C ALA* 3.4 1.0 + - - -
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 3.3 22.9 - - + +
116C HIS* 4.2 11.7 + - - +
117C GLU 3.3 9.6 - - - +
118C ARG* 2.9 26.8 + - - +
151C ALA* 4.4 13.7 - - + +
153C THR* 3.0 12.2 + - - -
154C SER 3.0 16.5 + - - -
155C ALA* 3.3 23.9 - - + +
156C PHE* 3.4 9.4 + - - +
213C HIS* 1.3 70.6 - - - +
215C ALA* 1.3 64.3 + - - +
216C VAL* 3.5 10.8 + - + -
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Residues in contact with ALA 215 (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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101B PHE* 4.1 6.5 - - + -
113C VAL 4.0 0.2 - - - +
114C THR* 2.6 32.9 + - - -
115C ASN* 4.2 6.7 + - - +
117C GLU 2.9 16.7 + - - +
119C MET* 3.9 19.3 - - + -
124C VAL* 3.9 30.5 - - + -
127C LEU* 4.5 8.5 - - + -
213C HIS 3.4 0.8 + - - -
214C THR* 1.3 70.8 - - - +
216C VAL* 1.3 56.9 + - - +
217C CYS* 4.2 1.1 - - - -
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 4.0 21.8 - - + -
113C VAL 3.4 8.7 - - - +
114C THR* 4.1 9.6 - - - -
124C VAL* 4.4 3.8 - - - +
128C CYS* 4.0 1.1 - - - -
135C VAL* 3.8 8.0 - - - +
136C ALA* 2.9 42.3 + - + +
147C ILE* 4.4 9.2 - - + -
150C VAL* 4.3 7.4 - - + -
151C ALA* 3.8 17.0 - - + -
155C ALA* 3.8 26.9 - - + -
156C PHE 4.9 4.5 + - - +
214C THR* 3.5 4.4 + - + +
215C ALA* 1.3 78.3 - - - +
217C CYS* 1.3 63.1 + - - +
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Residues in contact with CYS 217 (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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101B PHE* 3.9 24.5 - - + -
111C PHE 3.9 0.5 - - - +
112C PHE* 3.4 5.7 - - - +
113C VAL 2.9 34.2 + - - +
127C LEU* 4.6 2.7 - - - -
128C CYS* 2.0 57.0 - - + -
131C LEU* 4.4 5.6 - - - -
134C THR 3.4 1.1 - - - +
136C ALA 4.5 0.2 - - - -
215C ALA* 5.3 0.4 - - - -
216C VAL* 1.3 76.7 - - - +
218C GLU* 1.3 62.5 + - - +
219C PHE* 4.0 23.4 - - + -
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Residues in contact with GLU 218 (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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110C LYS* 3.0 33.5 - - + -
111C PHE 3.6 3.8 - - - +
112C PHE* 3.6 18.0 - - + -
133C GLY* 3.3 8.1 - - - -
134C THR* 2.7 47.3 + - - +
135C VAL 4.1 1.4 - - - +
136C ALA* 3.8 4.1 - - - -
137C ILE* 3.0 36.9 + - - +
139C ARG* 5.5 4.9 + - - -
217C CYS* 1.3 74.8 - - - +
219C PHE* 1.3 74.8 + - - +
220C PRO* 4.7 0.9 - - - +
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Residues in contact with PHE 219 (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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98B LEU* 3.5 37.7 - - + -
101B PHE* 5.7 0.2 - + - -
110C LYS* 3.2 8.0 - - - +
111C PHE* 3.1 63.7 + + + -
113C VAL* 4.1 13.9 - - + -
131C LEU* 3.3 34.1 - - + -
132C ARG 4.1 5.6 - - - -
133C GLY* 3.6 15.5 - - - -
217C CYS* 4.0 26.0 - - + -
218C GLU* 1.3 80.8 - - - +
220C PRO* 1.3 75.4 - - + +
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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