Contacts of the strand formed by residues 211 - 216 (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 THR 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE* 4.3 0.2 - - - -
193A GLU* 3.6 27.3 + - - +
194A ALA* 3.9 8.7 + - - +
197A SER* 3.1 35.1 + - - -
208A VAL* 3.8 5.6 - - + -
209A PRO 2.8 17.3 - - - +
210A ARG* 1.3 72.6 - - - +
212A LYS* 1.3 69.7 + - - +
259A SER* 4.2 8.0 - - - -
260A PHE 3.3 4.7 + - - -
261A GLN* 3.4 39.0 - - - +
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Residues in contact with LYS 212 (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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104A PHE* 3.6 31.9 - - + -
106A GLU* 3.8 20.5 + - - +
107A ASP* 4.1 27.9 + - - +
110A PHE* 3.7 29.1 - - + -
194A ALA* 4.4 9.0 - - - -
197A SER* 5.7 1.2 + - - -
201A GLN* 6.0 3.4 - - - +
210A ARG* 5.0 8.2 - - + +
211A THR* 1.3 81.5 + - - +
213A VAL* 1.3 64.7 + - - +
214A VAL* 3.5 0.9 + - - -
259A SER* 3.4 2.4 - - - -
260A PHE* 2.8 32.6 + - - +
404A LEU* 6.2 0.2 - - - -
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Residues in contact with VAL 213 (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 ASN* 4.8 0.7 - - - +
104A PHE* 3.7 13.7 - - - -
190A TYR* 4.0 13.7 - - + +
191A LEU* 3.8 27.6 - - + -
194A ALA* 3.9 10.1 - - + +
212A LYS* 1.3 72.2 - - - +
214A VAL* 1.3 64.1 + - - +
215A TYR* 4.9 7.9 - - + +
257A VAL* 3.5 31.2 - - + -
258A GLY 3.4 6.3 - - - +
259A SER* 5.6 0.2 - - - -
404A LEU* 3.9 17.3 - - + +
407A LYS* 4.2 25.3 - - + -
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Residues in contact with VAL 214 (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 ASN* 3.6 14.4 - - - +
104A PHE* 3.9 22.0 - - + -
110A PHE* 3.9 12.8 - - + -
114A VAL* 4.3 7.6 - - + -
151A PHE* 3.5 4.9 - - + -
212A LYS 3.5 2.0 + - - +
213A VAL* 1.3 79.5 - - - +
215A TYR* 1.3 80.3 + - - +
216A LEU* 4.0 7.4 - - + -
256A LYS 3.4 1.6 - - - +
257A VAL* 3.5 0.9 - - - -
258A GLY 2.8 32.3 + - - +
260A PHE* 3.6 43.7 - - + -
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Residues in contact with TYR 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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96A GLN* 3.5 21.8 + - - -
99A ARG* 3.6 49.3 + - + -
100A GLU* 3.6 32.9 - - + +
102A ASN* 2.7 38.3 + - - +
118A GLU* 4.8 0.3 - - - +
213A VAL* 4.9 7.1 - - + +
214A VAL* 1.3 76.4 - - - +
216A LEU* 1.3 67.7 + - - +
255A PRO* 3.9 10.8 - - + -
256A LYS 3.1 4.9 - - - -
257A VAL* 3.5 44.1 - - + +
407A LYS* 6.2 0.3 - - - +
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Residues in contact with LEU 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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102A ASN* 4.9 0.9 - - - +
114A VAL* 5.0 1.6 - - + -
117A ALA* 4.6 8.5 - - + -
118A GLU* 4.1 24.0 - - + -
121A ILE* 4.2 18.4 - - + -
127A PRO* 5.4 0.4 - - + -
140A VAL* 4.7 10.1 - - + -
151A PHE* 3.9 30.7 - - + -
214A VAL* 4.0 9.9 - - + -
215A TYR* 1.3 81.6 - - - +
217A ALA* 1.3 58.6 + - - +
221A PHE* 3.5 26.1 - - + -
255A PRO* 3.7 3.1 - - - -
256A LYS* 2.6 37.3 + - - +
260A PHE* 3.9 24.0 - - + -
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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