Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 2HNK
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 VAL 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 3.6 27.6 - - + +
51A PHE* 4.2 17.5 - - + -
52A LEU* 5.3 0.2 - - + -
178A ILE* 3.5 31.4 - - + -
179A ALA 3.3 6.7 - - - +
180A ASP* 3.8 5.4 - - - +
182A VAL* 3.6 3.7 - - - +
217A SER 3.7 0.7 - - - +
219A VAL* 2.7 40.1 + - - +
221A ILE* 3.6 31.9 - - + +
222A ALA* 4.7 0.2 - - + -
224A GLY* 1.3 78.6 - - - +
226A SER* 1.3 61.1 + - - +
227A LEU* 4.3 3.4 - - + -
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Residues in contact with SER 226 (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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177A LEU 3.4 1.9 - - - +
178A ILE* 3.4 5.7 - - - -
179A ALA* 2.8 38.6 + - - +
182A VAL* 3.5 20.1 - - - +
204A PHE* 4.9 3.3 - - - -
205A ASN* 4.5 2.6 + - - -
208A VAL* 5.9 0.2 - - - -
216A VAL* 4.1 7.5 - - - +
217A SER 3.4 4.3 - - - -
218A LEU* 3.4 29.2 - - - +
225A VAL* 1.3 72.6 - - - +
227A LEU* 1.3 62.3 + - - +
228A VAL* 3.8 17.2 - - - +
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Residues in contact with LEU 227 (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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51A PHE* 4.2 4.9 - - + -
55A LEU* 3.6 40.6 - - + -
176A LEU* 4.2 10.1 - - + -
177A LEU 3.6 2.0 - - - -
178A ILE* 3.9 20.6 - - + -
215A ASP 3.7 0.5 - - - +
216A VAL* 3.2 4.7 - - - -
217A SER 2.8 39.0 + - - +
219A VAL* 4.4 7.9 - - + -
225A VAL* 4.3 6.7 - - + -
226A SER* 1.3 77.2 - - - +
228A VAL* 1.3 59.5 + - - +
229A ARG 4.1 0.4 - - - -
51C PHE* 4.1 22.4 - - + -
54C ILE* 3.9 32.3 - - + +
55C LEU* 4.3 2.7 - - + -
58C ILE* 4.5 2.5 - - + -
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Residues in contact with VAL 228 (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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164A TYR* 4.3 12.6 - - + -
168A LEU* 5.3 1.8 - - + -
171A LEU* 4.9 1.0 - - - +
176A LEU* 3.6 2.8 - - - +
177A LEU* 2.6 64.8 + - + +
179A ALA* 5.3 0.2 - - + -
204A PHE* 4.8 1.6 - - + -
208A VAL* 3.7 33.4 - - + -
214A VAL* 3.8 30.3 - - + -
215A ASP 3.3 2.9 - - - +
216A VAL* 4.3 0.9 - - + -
226A SER* 4.0 19.7 - - - +
227A LEU* 1.3 78.0 - - - +
229A ARG* 1.3 60.7 + - - +
230A LYS 4.0 1.0 + - - -
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Residues in contact with ARG 229 (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 GLY* 3.8 25.3 + - - +
175A GLY 3.5 12.1 - - - +
176A LEU* 4.4 7.0 - - + -
214A VAL* 3.2 5.8 - - - -
215A ASP* 2.9 33.6 + - + +
228A VAL* 1.3 73.4 - - - +
230A LYS* 1.3 64.0 + - - +
231A ARG* 3.3 15.1 + - - +
232A LEU* 3.6 22.2 - - - +
1001A SO4 2.7 40.6 + - - -
54C ILE* 3.7 20.6 - - + +
57C LYS* 3.5 48.1 + - - +
58C ILE* 4.2 16.7 - - + +
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Residues in contact with LYS 230 (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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146A SER* 5.0 3.6 - - - -
168A LEU* 2.7 38.3 + - + +
169A LYS* 4.3 5.1 + - - +
171A LEU* 2.7 38.5 + - + +
172A LYS 3.4 19.9 - - - +
173A PRO* 4.2 9.6 - - + +
174A GLY* 2.6 34.5 + - - -
175A GLY 2.9 16.1 + - - +
213A LEU* 3.8 10.1 - - + +
214A VAL* 4.3 5.1 - - - +
228A VAL* 4.0 2.0 + - - +
229A ARG* 1.3 72.0 - - - +
231A ARG* 1.3 60.5 + - - +
233A GLU* 3.9 21.3 + - - -
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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