Contacts of the strand formed by residues 269 - 274 (chain B) in PDB entry 3HN3
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 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ARG* 3.1 43.5 - - + +
262B LEU 3.4 6.5 - - - +
263B LEU* 3.4 19.5 - - + -
267B ASN 3.8 2.4 + - - +
268B LYS* 1.3 80.6 - - - +
270B VAL* 1.3 60.7 + - - +
271B ALA 3.7 23.6 - - - +
272B ASN* 4.7 7.2 - - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 2.8 29.8 + - + +
264B ASP* 3.9 21.5 - - + +
268B LYS* 3.6 20.9 - - - +
269B VAL* 1.3 74.6 - - - +
271B ALA* 1.3 62.9 + - + +
281B LYS 4.2 5.4 - - - +
282B VAL* 4.1 12.1 - - + -
283B PRO* 4.4 11.0 - - + +
301B TYR* 3.9 28.7 - - + -
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ARG* 3.5 0.9 - - - -
262B LEU* 2.8 33.9 + - + +
269B VAL* 3.6 6.8 - - - +
270B VAL* 1.3 86.5 - - + +
272B ASN* 1.3 66.2 + - - +
280B LEU* 4.0 21.8 - - + -
281B LYS 3.5 22.2 - - - +
282B VAL* 4.8 2.0 - - + -
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Residues in contact with ASN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B VAL 3.2 14.8 - - - +
261B ARG* 4.1 14.6 - - + -
269B VAL* 4.7 7.2 - - + +
271B ALA* 1.3 79.4 - - - +
273B GLY* 1.3 63.4 + - - +
274B THR* 5.8 0.2 - - - +
280B LEU* 3.4 13.3 - - - +
650B NAG 1.5 76.6 + - - +
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Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TYR* 3.9 5.6 - - - -
259B GLU* 3.6 2.4 - - - +
260B VAL* 2.9 36.8 + - - +
272B ASN* 1.3 79.1 + - - +
274B THR* 1.3 70.0 + - - +
280B LEU* 3.6 5.3 - - - +
650B NAG 3.6 13.7 - - - -
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TYR* 2.8 20.3 + - - -
258B LEU 3.2 16.6 - - - +
259B GLU* 4.3 12.1 - - + +
260B VAL* 4.6 1.1 - - - +
272B ASN* 5.8 0.2 - - - +
273B GLY* 1.3 79.9 - - - +
275B GLY* 1.3 66.4 + - - +
277B GLN 4.1 5.5 - - - +
650B NAG 4.0 19.0 - - + +
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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