Contacts of the strand formed by residues 312 - 325 (chain B) in PDB entry 1NYE
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 GLY 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LYS* 3.3 5.4 - - - -
309B VAL 2.6 32.7 + - - -
310B ASP 3.0 2.0 + - - +
311B ALA* 1.3 81.8 - - - +
313B PHE* 1.3 56.5 - - - -
614D ASN* 3.0 11.6 - - - +
615D LEU 2.8 15.0 - - - -
618D GLN* 2.9 17.4 + - - +
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Residues in contact with PHE 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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23A ILE* 4.4 7.9 - - + -
144A GLY 5.7 0.3 - - - +
146A PRO* 3.9 22.6 - - + +
149A GLN* 5.5 1.6 + - - -
260B PHE* 3.5 30.7 - + + -
306B LEU* 3.4 33.9 - - + -
307B ASP 3.3 17.7 - - - -
308B LYS* 3.8 20.0 - - + -
309B VAL* 4.9 0.4 - - - -
312B GLY* 1.3 77.0 - - - -
314B ALA* 1.3 62.6 + - - +
614D ASN* 3.6 12.3 + - - +
615D LEU 3.5 5.9 + - - +
617D PHE* 4.0 11.2 - + + -
618D GLN* 3.3 36.6 - - + -
621D MET* 3.8 25.1 - - + -
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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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146A PRO* 4.7 5.2 - - - -
149A GLN* 6.2 4.5 - - + -
150A VAL* 5.8 0.2 - - - -
306B LEU* 3.3 6.9 - - - +
307B ASP 3.0 30.3 + - - +
309B VAL* 4.1 15.3 - - + -
313B PHE* 1.3 77.6 - - - +
315B ILE* 1.3 62.5 - - - +
316B THR* 3.1 20.7 + - + +
614D ASN* 4.8 6.1 - - - +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 4.1 7.2 - - + -
147A VAL* 4.1 12.1 - - + -
150A VAL* 3.2 44.7 - - + +
269B GLU* 3.8 21.5 - - + +
272B ILE* 4.0 25.4 - - + -
304B VAL* 3.7 24.2 - - + -
305B SER 3.3 7.0 - - - +
306B LEU* 3.9 16.8 - - + -
314B ALA* 1.3 70.9 - - - +
316B THR* 1.3 61.0 + - - +
317B LYS 4.9 0.4 - - - +
318B ILE* 4.7 8.1 - - + -
352B LYS* 5.8 0.9 - - - +
353B ALA* 3.5 17.3 - - + +
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Residues in contact with THR 316 (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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305B SER* 3.3 6.4 + - - -
307B ASP* 2.8 29.0 + - + +
309B VAL* 3.9 24.7 - - + -
314B ALA* 3.1 19.5 + - + +
315B ILE* 1.3 74.6 - - - +
317B LYS* 1.3 65.2 + - - +
353B ALA* 3.2 5.3 - - - +
354B GLU* 2.7 26.3 + - - +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 6.4 1.1 - - - -
304B VAL* 4.3 0.5 - - - +
305B SER* 2.9 42.7 + - - +
315B ILE* 3.7 1.1 - - - +
316B THR* 1.3 86.4 + - - +
318B ILE* 1.3 73.5 + - - +
319B ALA* 4.1 14.9 - - - +
353B ALA* 4.2 0.4 - - - -
354B GLU* 3.1 38.1 + - + +
356B THR* 3.7 29.7 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE* 4.5 14.8 - - + -
276B HIS* 3.3 26.7 - - + +
302B ALA* 4.3 18.2 - - + -
303B ASP 3.3 8.3 - - - +
304B VAL* 4.3 18.2 - - + -
315B ILE* 4.7 4.7 - - + -
317B LYS* 1.3 84.9 - - - +
319B ALA* 1.3 62.9 + - - +
320B LEU* 4.9 0.7 - - + -
351B LEU* 3.5 34.3 - - + -
353B ALA* 4.3 17.0 - - + -
354B GLU 2.7 10.3 + - - +
355B ILE* 3.2 10.0 - - + +
356B THR 3.2 21.3 + - - -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR 3.3 5.0 - - - +
302B ALA* 3.4 0.8 - - - -
303B ASP* 2.9 50.0 + - + +
317B LYS* 4.1 14.2 - - - +
318B ILE* 1.3 69.9 - - - +
320B LEU* 1.3 62.3 + - - +
321B LYS* 3.7 1.7 + - + +
356B THR* 3.4 17.0 - - - +
358B ASP* 5.6 3.6 - - - +
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Residues in contact with LEU 320 (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 HIS* 4.0 33.4 - - + +
277B ALA* 4.6 5.4 - - - -
280B PHE* 4.2 33.7 - - + -
300B THR* 4.9 1.8 - - - +
301B THR 3.4 3.4 - - - +
302B ALA* 4.1 17.9 - - + -
318B ILE* 4.9 0.7 - - + +
319B ALA* 1.3 73.6 - - - +
321B LYS* 1.3 60.2 + - - +
342B LYS* 3.8 20.9 - - + -
348B SER* 4.8 1.1 - - - +
355B ILE* 3.7 27.1 - - + -
356B THR 2.9 14.1 + - - +
357B LEU* 3.5 8.3 - - + +
358B ASP* 2.8 29.8 + - - +
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Residues in contact with LYS 321 (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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299B ASP 3.8 0.7 + - - +
300B THR* 2.9 3.8 - - - -
301B THR* 2.6 64.3 + - + +
319B ALA* 3.7 2.0 + - + +
320B LEU* 1.3 72.4 - - - +
322B SER* 1.3 63.5 + - - +
323B GLU* 3.6 30.9 + - - +
358B ASP* 3.3 19.7 - - + +
360B GLN* 6.0 0.8 - - - -
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PHE* 4.0 16.8 - - - -
284B LEU* 4.7 0.2 - - - +
299B ASP 3.1 3.8 - - - -
300B THR* 3.1 28.4 - - - +
321B LYS* 1.3 77.3 - - - +
323B GLU* 1.3 64.8 + - - +
324B VAL* 3.2 21.2 - - - +
357B LEU* 4.9 2.2 - - - -
358B ASP 2.7 12.6 + - - -
359B TYR* 2.9 38.4 - - - +
360B GLN* 3.1 3.3 + - - +
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Residues in contact with GLU 323 (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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297B SER* 4.2 1.0 - - - +
298B ILE* 3.8 1.4 - - - -
299B ASP* 2.6 49.7 + - + +
321B LYS* 3.6 23.6 + - - +
322B SER* 1.3 75.7 + - - +
324B VAL* 1.3 60.8 + - - +
325B ALA 4.3 0.2 + - - -
360B GLN* 2.9 37.2 - - + +
362B LYS* 3.7 23.9 + - - +
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Residues in contact with VAL 324 (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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284B LEU* 3.4 24.0 - - + -
288B LEU* 4.8 0.4 - - + -
295B PRO* 4.7 0.2 - - + -
297B SER 3.6 10.1 - - - +
298B ILE* 3.8 16.6 - - + -
322B SER* 3.2 25.4 - - - +
323B GLU* 1.3 73.2 - - - +
325B ALA* 1.3 59.4 + - - +
326B VAL* 3.6 24.0 - - + -
334B PHE* 3.7 23.1 - - + -
338B ILE* 5.2 1.6 - - + -
359B TYR* 5.5 2.7 - - + -
360B GLN 3.0 9.0 + - - +
361B LEU* 2.8 26.1 - - + +
362B LYS* 2.9 15.5 + - - +
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Residues in contact with ALA 325 (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 THR* 3.0 41.1 + - - +
297B SER* 3.0 20.2 + - - +
323B GLU 4.3 0.2 + - - -
324B VAL* 1.3 73.1 - - - +
326B VAL* 1.3 66.8 + - - +
327B PRO* 4.5 0.2 - - - -
362B LYS* 4.0 28.3 - - + +
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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