Contacts of the strand formed by residues 214 - 220 (chain A) in PDB entry 2PKW
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 ARG 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS 4.0 3.4 + - - -
81A ALA 2.8 38.3 + - - -
82A VAL 4.2 7.4 + - - -
83A GLY* 3.5 21.7 - - - +
166A GLN 2.8 11.1 + - - -
167A VAL* 3.0 16.3 - - + +
168A VAL 2.9 23.2 + - - -
211A ALA* 3.3 5.8 - - - +
213A LYS* 1.3 78.8 - - + +
215A VAL* 1.3 71.8 + - - +
216A VAL* 4.1 6.1 - - + -
244A ILE* 3.4 39.0 - - + +
245A TYR 3.4 5.8 - - - +
247A GLY 4.4 1.1 - - - +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.2 13.5 - - + +
170A LEU* 4.1 13.9 - - + -
204A LEU* 4.2 8.5 - - + -
207A ALA* 3.2 47.6 - - + +
208A ARG* 3.7 12.3 - - + -
211A ALA* 3.7 6.1 - - + -
214A ARG* 1.3 80.8 - - - +
216A VAL* 1.3 63.7 + - - +
217A VAL* 4.2 11.4 - - + -
243A ASP 3.6 1.0 - - - +
244A ILE* 3.4 4.7 - - - -
245A TYR* 2.9 41.8 + - + +
246A ALA 4.6 3.1 - - - +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 5.2 0.2 - - + -
81A ALA* 3.5 50.9 - - + +
82A VAL* 3.7 18.6 - - + -
167A VAL* 4.1 8.3 - - + -
168A VAL 2.9 6.5 + - - +
169A TYR* 3.6 16.1 - - + -
170A LEU* 2.8 27.9 + - - +
214A ARG* 4.1 4.9 - - - -
215A VAL* 1.3 76.6 - - - +
217A VAL* 1.3 64.7 + - - +
218A LYS 4.2 0.2 - - - -
242A PHE* 3.6 23.1 - - + -
243A ASP 3.4 5.4 - - - +
244A ILE* 5.1 1.6 - - + -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 3.3 24.2 - - + +
172A PRO* 5.0 1.8 - - + -
204A LEU* 4.4 2.0 - - + -
215A VAL* 4.2 11.2 - - + -
216A VAL* 1.3 79.2 - - - +
218A LYS* 1.3 66.7 + - - +
219A ARG* 3.5 30.3 + - + +
226A LEU* 4.0 24.7 - - + +
242A PHE* 3.4 3.8 - - - -
243A ASP* 2.9 42.9 + - + +
245A TYR* 4.0 21.3 - - + -
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP* 4.1 13.7 + - - -
169A TYR* 3.3 27.5 - - - +
170A LEU 2.8 9.2 + - - +
171A ASP* 3.7 36.0 + - + +
172A PRO* 4.9 0.9 - - - +
216A VAL 4.2 0.6 - - - -
217A VAL* 1.3 74.4 - - - +
219A ARG* 1.3 75.5 + - - +
220A PRO* 4.6 1.1 - - - +
240A HIS* 3.4 44.5 + - + -
241A ARG 3.6 4.3 - - - +
242A PHE* 3.5 21.0 - - + -
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO* 4.0 24.0 + - - +
174A PHE* 3.6 41.1 - - - +
200A ALA* 5.5 2.0 - - - +
201A ASP* 5.4 0.4 + - - -
217A VAL* 3.6 21.4 - - + +
218A LYS* 1.3 87.9 + - - +
220A PRO* 1.3 77.0 - - + +
223A ALA* 4.6 1.6 - - + -
224A PRO 3.3 25.7 + - - -
225A PRO 4.4 0.2 - - - -
226A LEU* 3.9 32.6 - - - +
240A HIS* 3.1 4.6 - - - +
241A ARG* 2.8 56.1 + - - +
243A ASP* 3.5 19.1 - - - +
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 3.8 40.2 - - + -
176A HIS* 4.6 14.4 - - + +
218A LYS 4.6 1.8 - - - +
219A ARG* 1.3 89.5 - - + +
221A ASP* 1.3 69.6 + - - +
222A TYR 3.5 0.3 + - - -
223A ALA* 3.0 34.6 + - + +
239A GLY 3.8 3.1 - - - +
240A HIS* 3.8 10.8 - - + -
241A ARG* 3.6 4.7 + - - -
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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