Contacts of the strand formed by residues 307 - 315 (chain B) in PDB entry 1NTZ
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 PHE 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 3.4 41.2 + + - -
299B VAL* 3.6 26.7 - - + -
300B ALA* 3.6 35.9 - - + -
303B VAL* 4.3 12.8 - - + -
305B GLN* 3.1 39.8 + - - +
306B PRO* 1.3 75.0 - - - +
308B ASP* 1.3 71.0 + - - +
309B VAL* 3.8 17.3 - - + -
327B ILE* 3.2 15.0 - - - +
328B SER* 4.3 8.5 - - - +
336B VAL* 4.6 7.4 - - + -
31I GLN 3.0 16.5 - - - +
32I ALA* 4.3 5.9 - - - +
35I PRO* 4.0 8.5 + - - +
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Residues in contact with ASP 308 (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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296B TYR* 3.4 2.9 - - - -
307B PHE* 1.3 81.1 - - - +
309B VAL* 1.3 81.4 + - - +
326B THR* 3.4 4.7 - - - -
327B ILE* 2.9 36.0 + - + +
336B VAL* 4.7 0.7 - - - +
28I PRO* 3.1 12.9 - - + +
29I LEU 2.8 27.0 + - - +
30I VAL 3.7 0.2 + - - -
31I GLN* 2.5 56.3 + - - +
32I ALA* 3.7 13.7 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLY 4.7 0.2 - - - +
281B ALA 4.7 1.0 - - - +
293B SER* 5.2 2.9 + - - -
295B LEU* 4.0 13.9 - - + +
296B TYR* 3.7 42.3 - - + +
299B VAL* 4.1 16.6 - - + -
307B PHE* 3.8 9.6 - - + -
308B ASP* 1.3 83.8 + - - +
310B SER* 1.3 63.1 + - - +
324B PHE* 5.2 0.9 - - + -
325B TYR 3.3 6.7 - - - +
326B THR* 3.6 24.7 - - + -
336B VAL* 4.4 1.8 - - + -
340B ALA* 4.6 8.1 - - + -
28I PRO* 3.6 2.7 - - - -
31I GLN* 3.0 19.4 + - - +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLY 3.4 12.9 + - - -
281B ALA* 3.6 17.7 - - - -
282B GLY* 4.5 0.8 + - - -
295B LEU* 3.9 7.9 - - - -
309B VAL* 1.3 80.4 - - - +
311B ALA* 1.3 75.1 + - - +
324B PHE* 3.2 1.2 - - - +
325B TYR* 2.8 32.9 + - - +
26I LEU* 6.0 1.4 - - - +
27I ARG* 4.4 4.1 + - - -
28I PRO* 3.3 27.0 - - - +
31I GLN* 4.7 1.6 - - - -
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Residues in contact with ALA 311 (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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276B GLN* 3.8 40.7 - - + +
279B LEU* 4.2 14.8 - - + -
280B GLY 2.7 16.6 + - - +
281B ALA* 4.7 1.2 - - - -
295B LEU* 3.7 4.4 - - + +
310B SER* 1.3 88.2 + - - +
312B PHE* 1.3 59.2 + - - +
322B PHE* 4.3 4.9 - - + -
323B GLY 3.2 12.6 - - - +
324B PHE* 4.0 3.4 - - - +
26I LEU 5.6 0.5 - - - +
27I ARG* 5.3 3.6 + - - -
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Residues in contact with PHE 312 (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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160B ILE* 3.5 26.7 - - + -
163B LEU* 4.1 21.3 - - + -
164B HIS* 4.8 2.0 - + - -
256B ALA* 5.9 0.9 - - + -
258B VAL* 3.7 19.1 - - + -
276B GLN* 5.1 0.2 - - - -
311B ALA* 1.3 74.5 - - - +
313B ASN* 1.3 64.6 + - - +
314B ALA* 3.8 23.6 - - + -
321B LEU* 4.0 9.0 - - + -
322B PHE* 3.3 7.8 - - - -
323B GLY 2.7 43.4 + - - +
324B PHE* 4.3 10.5 - - - +
325B TYR* 4.6 11.2 - + + +
9I GLY* 3.1 33.9 - - - -
10I PRO* 4.3 3.4 - - + -
26I LEU 3.3 17.3 - - - -
27I ARG* 4.8 4.9 - - - -
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Residues in contact with ASN 313 (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 SER* 4.7 3.2 + - - -
269B ALA 5.1 0.5 + - - +
272B PHE* 4.1 15.9 - - - +
273B SER* 3.8 19.8 + - - -
276B GLN* 3.7 25.4 + - + +
312B PHE* 1.3 81.8 - - - +
314B ALA* 1.3 70.5 + - - +
315B SER* 4.2 3.9 + - - -
321B LEU 3.5 2.6 + - - -
322B PHE* 3.8 27.6 - - + +
7I ARG* 4.0 18.7 - - - +
8I SER 2.6 29.5 + - - +
9I GLY* 4.4 1.5 - - - -
10I PRO* 3.6 3.1 - - - +
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Residues in contact with ALA 314 (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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164B HIS* 4.8 1.1 - - - +
261B SER* 4.3 0.3 + - - -
312B PHE* 3.8 18.8 - - + -
313B ASN* 1.3 76.6 + - - +
315B SER* 1.3 61.9 + - - +
316B TYR* 3.7 21.1 - - + +
320B GLY* 3.3 2.5 - - - -
321B LEU* 2.7 43.8 + - + +
10I PRO* 3.5 23.3 - - + -
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Residues in contact with SER 315 (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 ALA 3.0 21.4 + - - -
263B ALA 3.5 0.2 - - - -
264B ILE* 3.0 34.7 + - - +
269B ALA* 4.5 3.5 - - - +
313B ASN* 4.2 5.7 + - - -
314B ALA* 1.3 75.8 - - - +
316B TYR* 1.3 62.6 + - - +
319B SER 4.1 1.8 - - - -
320B GLY* 4.3 0.4 - - - -
4I VAL* 2.8 36.0 + - - +
7I ARG* 4.0 16.5 - - - +
10I PRO* 4.3 0.6 - - - +
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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