Contacts of the strand formed by residues 299 - 305 (chain B) in PDB entry 2NTZ
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 ALA 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A PHE* 5.3 2.9 - - + -
304A PHE 3.0 15.7 - - - +
305A ASN* 2.7 26.5 - - + +
306A ARG 4.4 0.2 - - - +
294B ARG* 4.1 0.3 - - - +
295B VAL* 3.6 2.3 - - - +
296B LYS* 2.7 47.2 + - + +
297B GLY 3.1 2.2 + - - -
298B ARG* 1.3 70.3 - - - +
300B PHE* 1.3 62.8 + - - +
32E C 6.1 0.4 - - - +
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Residues in contact with PHE 300 (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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304A PHE* 2.9 59.2 + + + +
305A ASN* 5.7 0.2 - - - -
307A LEU* 4.1 28.3 - - + -
311A LEU* 5.0 0.4 - - + -
312A GLN* 3.2 56.3 - - + +
315A LEU* 3.6 23.6 - - + -
293B LYS* 4.6 1.8 - - - -
294B ARG 3.2 9.9 - - - +
295B VAL* 4.3 8.3 - - + -
298B ARG 5.6 0.4 - - - -
299B ALA* 1.3 79.3 - - - +
301B SER* 1.3 63.2 + - - +
302B TYR* 3.4 35.0 - + - -
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Residues in contact with SER 301 (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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302A TYR 3.0 16.4 - - - -
303A GLU* 3.7 21.4 - - - +
304A PHE* 4.7 0.4 - - - -
293B LYS* 3.5 1.6 - - - +
294B ARG* 2.7 50.2 + - - +
300B PHE* 1.3 81.5 - - - +
302B TYR* 1.3 66.4 + - - +
303B GLU* 3.1 20.8 + - - +
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Residues in contact with TYR 302 (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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301A SER* 3.2 5.0 - - - -
302A TYR* 2.8 40.9 + - + +
304A PHE* 4.8 7.2 - + - -
312A GLN* 3.8 0.7 + - - -
315A LEU* 4.1 10.2 - - + +
316A ASP* 2.6 51.0 + - - -
319A ILE* 4.2 26.5 - - + -
281B LEU* 4.2 14.8 - - + -
292B ARG 3.4 5.6 - - - +
293B LYS* 3.8 23.6 - - + -
300B PHE* 3.4 37.8 - + - -
301B SER* 1.3 78.6 + - - +
303B GLU* 1.3 65.1 + - - +
304B PHE* 3.9 18.6 - - + -
319B ILE* 5.9 0.7 - - + -
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Residues in contact with GLU 303 (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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300A PHE 3.8 0.9 - - - +
301A SER* 3.6 17.6 - - - +
303A GLU* 5.2 4.0 - - - +
278B VAL* 5.7 0.2 - - - +
290B PHE* 3.2 18.3 - - + -
292B ARG* 2.8 55.3 + - + +
294B ARG* 3.1 47.4 + - + -
301B SER* 3.1 22.8 + - - +
302B TYR* 1.3 80.3 - - - +
304B PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 304 (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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299A ALA* 3.7 2.3 - - - +
300A PHE* 2.7 53.9 + + + +
302A TYR* 4.0 19.7 - + - -
319A ILE* 3.8 30.7 - - + -
323A LEU* 4.4 7.0 - - + -
281B LEU* 5.0 2.5 - - + -
290B PHE* 3.0 8.3 - - - -
291B ALA* 3.6 25.8 - - + -
292B ARG 5.0 2.2 - - - -
302B TYR* 3.9 27.6 - + + -
303B GLU* 1.3 77.2 - - - +
305B ASN* 1.3 67.2 + - - +
307B LEU* 3.3 25.8 - - + -
315B LEU* 3.9 19.3 - - + -
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Residues in contact with ASN 305 (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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296A LYS* 5.7 0.4 - - - +
298A ARG* 3.9 4.2 + - - +
299A ALA* 3.0 27.9 - - + +
300A PHE* 5.3 1.3 - - - -
288B ASP* 4.3 1.6 - - - +
289B ARG* 3.5 14.2 + - - -
290B PHE* 2.6 55.8 + - + +
304B PHE* 1.3 80.4 - - - +
306B ARG* 1.3 93.8 + - - +
307B LEU* 3.6 5.1 - - - +
32Y C 4.6 12.1 + - - -
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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