Contacts of the strand formed by residues 256 - 262 (chain A) in PDB entry 4HNE
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 LYS 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.4 9.7 - - + -
153A PRO* 3.9 15.3 - - + -
155A ASN* 3.0 39.0 + - - +
156A GLU* 2.6 28.7 + - - +
215A TYR* 3.1 5.2 - - - -
216A LEU 2.6 35.2 + - - +
221A PHE* 4.0 14.4 - - + -
222A ASN 2.7 23.8 + - - -
223A TYR* 3.7 33.7 - - + +
255A PRO* 1.3 75.3 - - - +
257A VAL* 1.3 68.0 + - - +
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Residues in contact with VAL 257 (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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151A PHE* 4.2 0.2 - - - -
153A PRO* 3.4 4.0 - - - +
154A LYS* 2.9 51.5 + - + -
155A ASN* 4.8 0.9 + - - -
190A TYR* 4.2 10.8 - - + +
213A VAL* 3.5 28.3 - - + -
214A VAL 3.5 3.8 - - - +
215A TYR* 3.5 40.3 - - + +
255A PRO 4.1 0.8 + - - -
256A LYS* 1.3 77.0 - - - +
258A GLY* 1.3 60.4 + - - +
409A PRO* 6.4 1.1 - - + -
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Residues in contact with GLY 258 (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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151A PHE* 3.7 12.3 - - - -
152A LYS 3.2 14.8 - - - -
153A PRO* 3.9 0.4 - - - -
154A LYS 4.0 2.9 - - - -
190A TYR* 4.0 11.4 - - - -
213A VAL* 3.4 6.8 - - - +
214A VAL 2.8 30.8 + - - -
256A LYS 3.7 0.4 + - - -
257A VAL* 1.3 77.5 - - - +
259A SER* 1.3 61.2 + - - -
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Residues in contact with SER 259 (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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150A VAL 3.5 1.8 + - - +
151A PHE* 3.1 8.9 - - - -
152A LYS* 3.0 46.0 + - - +
190A TYR* 3.6 28.7 - - - +
193A GLU* 3.5 25.8 - - - +
194A ALA 4.8 0.4 - - - -
211A THR* 4.2 7.0 - - - -
212A LYS 3.4 7.0 - - - -
213A VAL* 4.7 0.4 - - - +
258A GLY* 1.3 73.9 - - - -
260A PHE* 1.3 57.8 + - - +
261A GLN* 4.1 1.5 - - - +
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Residues in contact with PHE 260 (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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110A PHE* 3.2 37.5 - + - -
113A VAL* 4.1 17.7 - - + -
114A VAL* 3.9 23.3 - - + -
117A ALA* 3.9 24.0 - - + -
140A VAL* 4.1 4.7 - - + -
148A ILE* 4.8 0.2 - - + -
149A ALA* 3.5 29.4 - - + -
150A VAL 3.5 2.5 - - - -
151A PHE* 3.8 19.1 - + + -
211A THR* 3.3 11.7 - - - -
212A LYS 2.8 8.5 + - - +
214A VAL* 3.6 31.6 - - + -
216A LEU* 3.9 21.3 - - + -
259A SER* 1.3 72.3 - - - +
261A GLN* 1.3 58.9 + - - +
262A LEU* 4.6 1.8 - - + -
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Residues in contact with GLN 261 (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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149A ALA* 3.0 6.0 - - - -
150A VAL* 2.8 49.2 + - + +
193A GLU* 3.9 13.9 + - + +
208A VAL* 4.4 2.8 - - - +
209A PRO* 3.5 23.6 + - + +
211A THR* 3.4 27.1 + - + +
259A SER* 4.1 0.6 - - - +
260A PHE* 1.3 73.1 - - - +
262A LEU* 1.3 70.2 - - - +
344A ALA 4.3 5.1 + - - -
345A ILE* 3.2 34.0 + - - +
347A ASN* 4.4 1.6 + - - -
500A ADP 2.7 30.5 + - - +
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Residues in contact with LEU 262 (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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109A GLU* 6.1 1.6 - - + +
110A PHE* 4.0 19.1 - - + -
113A VAL* 3.7 43.3 - - + -
148A ILE 3.8 4.9 - - - +
209A PRO* 3.3 18.6 - - + +
210A ARG* 3.0 58.0 + - + +
260A PHE* 4.0 2.6 + - + -
261A GLN* 1.3 72.1 - - - +
263A PHE* 1.3 63.1 + - - +
264A VAL* 4.8 2.5 - - + -
500A ADP 3.0 18.7 + - - -
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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