Contacts of the strand formed by residues 299 - 309 (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 GLU 299 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292I VAL 4.6 0.4 - - - +
293I TYR* 3.4 22.3 - - - +
294I LYS* 3.3 50.5 + - + +
297I GLY* 3.7 1.0 - - - -
298I ARG* 1.3 83.3 + - - +
300I LEU* 1.3 61.9 + - - +
301I THR* 5.6 2.9 - - - +
366I LYS* 3.7 16.9 + - + +
367I ILE 3.3 3.8 - - - +
368I GLN* 3.6 34.9 + - + +
372I TRP* 4.1 7.4 + - - -
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Residues in contact with LEU 300 (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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292I VAL 3.4 26.9 - - - +
293I TYR* 3.9 9.2 - - + -
299I GLU* 1.3 76.2 - - - +
301I THR* 1.3 60.8 + - - +
302I ILE* 3.9 26.0 - - + -
319I TYR* 4.8 7.2 - - + +
366I LYS* 3.5 1.1 - - - -
367I ILE* 2.6 68.2 + - + +
372I TRP* 4.0 22.9 - - + -
388I ILE* 3.9 34.1 - - + -
410I VAL* 4.3 5.6 - - + -
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Residues in contact with THR 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I GLY* 3.2 3.5 - - - -
292I VAL* 2.8 45.4 + - + +
299I GLU* 5.6 4.0 - - - +
300I LEU* 1.3 73.3 + - - +
302I ILE* 1.3 64.7 + - - +
303I ASN* 4.8 5.8 - - - +
364I VAL* 4.0 20.2 - - + -
365I VAL 3.3 8.5 - - - +
366I LYS* 4.1 15.8 - - + +
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Residues in contact with ILE 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I LEU* 3.6 25.4 - - + -
290I GLY 3.6 2.2 - - - -
291I GLY* 3.9 11.9 - - - -
300I LEU* 3.9 22.0 - - + -
301I THR* 1.3 81.2 - - - +
303I ASN* 1.3 63.9 + - - +
304I VAL* 3.9 17.9 + - + -
319I TYR* 5.5 5.4 - - + -
363I ILE 3.7 0.5 - - - +
364I VAL* 3.6 0.9 - - - -
365I VAL* 2.7 58.8 + - + +
367I ILE* 3.9 22.0 - - + -
388I ILE* 5.2 4.0 - - + -
392I LEU* 5.5 7.4 - - + -
406I ILE* 4.8 11.9 - - + -
410I VAL* 4.4 5.4 - - + -
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Residues in contact with ASN 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I LEU* 3.5 7.3 - - - +
289I ASN* 2.9 47.9 + - - +
290I GLY* 3.1 11.7 + - - -
301I THR* 4.8 5.0 - - - +
302I ILE* 1.3 76.6 - - - +
304I VAL* 1.3 60.9 + - - +
305I LYS 4.2 0.4 - - - -
362I GLU* 3.3 26.0 + - + +
363I ILE 3.4 6.3 - - - +
364I VAL* 3.6 22.7 - - + +
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Residues in contact with VAL 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I THR* 3.5 39.9 - - + -
287I GLU 3.4 6.5 - - - +
288I LEU* 4.7 0.2 - - + -
302I ILE* 4.1 19.5 - - + +
303I ASN* 1.3 78.5 - - - +
305I LYS* 1.3 64.4 + - - +
306I VAL* 3.4 4.7 + - + -
361I LYS 3.3 3.8 - - - +
362I GLU* 3.2 4.1 - - - -
363I ILE* 2.8 45.8 + - + +
365I VAL* 4.0 24.0 - - + -
392I LEU* 4.1 10.5 - - + -
406I ILE* 3.9 9.0 - - + -
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Residues in contact with LYS 305 (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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285I THR 3.3 6.8 - - - +
286I THR* 3.4 0.9 - - - -
287I GLU* 2.9 52.4 + - + +
289I ASN* 3.3 32.3 - - + +
304I VAL* 1.3 69.6 - - - +
306I VAL* 1.3 62.8 + - - +
307I LYS* 5.4 0.2 - - - +
361I LYS 4.0 3.8 - - - -
362I GLU* 3.4 31.2 - - + +
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Residues in contact with VAL 306 (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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284I VAL* 3.6 25.8 - - + -
285I THR 3.5 3.4 - - - +
286I THR* 4.1 0.7 - - + -
304I VAL* 4.1 11.4 - - + +
305I LYS* 1.3 77.8 - - - +
307I LYS* 1.3 70.4 + - - +
308I ASN* 4.7 0.9 - - + -
355I ILE* 4.1 28.0 - - + -
360I ALA* 3.2 5.5 - - - +
361I LYS* 2.9 40.2 + - + +
363I ILE* 3.7 31.2 - - + -
394I PHE* 3.8 15.7 - - + -
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Residues in contact with LYS 307 (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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284I VAL* 3.3 8.3 - - - +
285I THR* 2.9 44.5 + - - +
306I VAL* 1.3 77.0 - - - +
308I ASN* 1.3 65.4 + - - +
309I ASN* 3.3 41.9 + - - +
358I GLY* 3.4 20.3 + - - +
359I GLU 3.7 7.6 - - - +
360I ALA* 3.7 22.0 - - + -
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Residues in contact with ASN 308 (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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283I ASN 3.8 1.6 - - - -
284I VAL* 4.5 4.9 - - + -
306I VAL* 4.7 1.1 - - + -
307I LYS* 1.3 79.4 - - - +
309I ASN* 1.3 55.1 + - - +
310I THR* 2.4 44.3 + - - +
312I GLN 3.0 20.0 + - - +
314I LEU* 3.4 27.4 - - + +
355I ILE* 4.3 8.1 - - + +
356I ALA* 2.9 31.4 - - + +
358I GLY* 2.5 30.9 + - - -
359I GLU 3.4 4.4 + - - +
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Residues in contact with ASN 309 (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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281I LYS 4.1 4.3 - - - +
282I GLU* 3.4 8.8 - - - +
283I ASN* 2.6 54.3 + - - +
285I THR* 3.8 15.2 + - - +
307I LYS* 3.3 43.1 + - - +
308I ASN* 1.3 65.3 + - - -
310I THR* 1.3 58.0 + - - +
358I GLY* 3.6 8.1 - - - +
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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