Contacts of the strand formed by residues 283 - 295 (chain I) in PDB entry 4PHZ
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 ASN 283 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276I THR 5.8 0.9 - - - +
278I GLY* 5.3 13.8 - - - +
279I VAL 4.8 6.5 + - - +
280I GLY 4.0 8.7 - - - +
281I LYS 3.7 10.7 - - - +
282I GLU* 1.3 78.3 - - - +
284I VAL* 1.3 63.2 + - - +
285I THR* 3.8 14.5 - - - +
308I ASN* 3.8 1.2 - - - -
309I ASN* 2.6 65.8 + - - +
310I THR* 3.2 11.4 + - - +
402I TYR* 4.5 5.4 - - - -
403I ALA 6.1 0.9 - - - +
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Residues in contact with VAL 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I ASN* 1.3 81.2 - - - +
285I THR* 1.3 69.5 + - - +
306I VAL* 3.6 23.8 - - + -
307I LYS 3.3 16.4 - - - +
308I ASN* 4.5 4.5 - - + -
314I LEU* 3.6 17.0 - - + -
394I PHE* 3.6 31.6 - - + -
402I TYR* 3.5 33.1 - - + +
403I ALA 4.6 4.0 + - - +
404I SER* 3.5 18.8 - - - -
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Residues in contact with THR 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I ASN* 3.8 17.7 - - - +
284I VAL* 1.3 79.7 - - - +
286I THR* 1.3 62.3 + - - +
287I GLU* 5.1 8.2 - - - +
305I LYS 3.3 4.9 - - - +
306I VAL* 3.5 1.4 - - - -
307I LYS* 2.9 46.4 + - - +
309I ASN* 3.8 6.9 + - - +
404I SER* 4.4 1.1 - - - -
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Residues in contact with THR 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I VAL* 4.8 0.2 - - + -
285I THR* 1.3 78.0 - - - +
287I GLU* 1.3 72.5 + - - +
288I LEU 4.4 0.3 + - - -
304I VAL* 3.5 25.8 - - + -
305I LYS 3.4 2.5 - - - -
306I VAL* 4.1 5.2 - - + -
392I LEU* 3.8 6.2 - - + +
394I PHE* 3.7 24.0 - - + -
404I SER* 2.6 28.3 + - - +
405I GLU 3.1 28.8 + - - +
406I ILE* 4.0 8.9 - - - +
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Residues in contact with GLU 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS* 5.0 9.5 + - - -
285I THR* 5.1 6.4 - - - +
286I THR* 1.3 89.3 + - - +
288I LEU* 1.3 67.8 + - - +
304I VAL* 3.4 4.0 - - - -
305I LYS* 2.9 53.4 + - + +
406I ILE* 3.7 2.9 - - - -
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Residues in contact with LEU 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I GLU* 1.3 79.5 + - - +
289I ASN* 1.3 62.4 + - - +
290I GLY 3.9 9.0 - - - +
302I ILE* 3.6 29.2 - - + -
303I ASN 3.5 16.4 - - - +
304I VAL* 4.7 0.2 - - + -
388I ILE* 3.7 19.7 - - + -
406I ILE* 3.3 27.2 - - + +
407I GLY* 3.7 15.8 + - - +
408I GLY* 3.7 33.9 - - - +
409I PRO* 4.2 3.6 - - + +
410I VAL* 4.1 11.7 - - + -
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Residues in contact with ASN 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288I LEU* 1.3 75.6 - - - +
290I GLY* 1.3 60.4 + - - +
303I ASN* 2.9 35.2 + - + +
305I LYS* 3.3 38.9 - - + +
362I GLU* 3.2 24.7 + - - +
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Residues in contact with GLY 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLY* 6.0 2.7 - - - -
288I LEU* 3.9 9.0 - - - +
289I ASN* 1.3 75.0 - - - +
291I GLY* 1.3 58.0 + - - -
302I ILE* 3.6 2.1 - - - -
303I ASN* 3.1 32.9 + - - +
409I PRO 4.7 7.8 + - - -
411I ILE* 6.4 0.9 - - - -
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Residues in contact with GLY 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I GLY* 1.3 73.9 - - - -
292I VAL* 1.3 70.8 + - - +
301I THR 3.2 11.0 - - - -
302I ILE* 3.9 3.6 - - - -
409I PRO 4.2 6.3 + - - -
410I VAL* 3.8 20.2 - - - -
411I ILE* 2.9 27.3 + - - +
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Residues in contact with VAL 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291I GLY* 1.3 81.0 - - - +
293I TYR* 1.3 63.1 + - - +
294I LYS* 5.5 4.5 - - + -
299I GLU 4.6 0.3 - - - -
300I LEU* 3.4 5.8 - - - +
301I THR* 2.8 45.7 + - + +
411I ILE* 3.1 18.8 - - + +
412I PRO 4.9 0.4 - - - -
413I LYS* 3.9 31.0 - - + +
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Residues in contact with TYR 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LEU* 5.0 1.0 - - - +
292I VAL* 1.3 74.1 - - - +
294I LYS* 1.3 61.0 + - - +
295I VAL* 3.6 22.0 - - + -
299I GLU 3.4 15.3 - - - +
300I LEU* 3.9 10.8 - - + -
372I TRP* 4.3 17.0 - + + +
378I SER* 4.2 9.2 - - - -
380I LEU* 3.6 27.3 + - + -
381I ALA* 3.6 20.2 - - - -
386I SER* 2.9 26.2 + - - -
410I VAL* 3.7 21.3 - - + -
411I ILE 3.0 16.1 + - - -
412I PRO* 3.3 35.1 - - + +
413I LYS 2.7 32.1 + - - -
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Residues in contact with LYS 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292I VAL* 5.5 4.0 - - + -
293I TYR* 1.3 79.5 - - - +
295I VAL* 1.3 62.1 + - - +
296I PRO* 3.3 12.3 - - - +
297I GLY* 3.1 27.8 + - - -
299I GLU* 3.3 49.3 + - + +
372I TRP* 5.2 0.9 + - - -
378I SER* 5.0 5.0 - - - -
413I LYS* 3.6 15.9 - - + -
415I VAL* 3.8 23.4 - - + +
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Residues in contact with VAL 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ARG* 5.6 0.3 + - - -
293I TYR* 3.6 29.8 - - + -
294I LYS* 1.3 77.1 - - - +
296I PRO* 1.4 67.5 + - + +
378I SER* 4.6 5.4 - - - +
381I ALA* 4.0 18.2 - - + -
412I PRO* 3.8 16.4 - - + -
413I LYS 2.9 8.8 + - - +
414I PHE* 3.5 31.8 - - + -
415I VAL* 2.9 25.5 + - - +
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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