Contacts of the strand formed by residues 401 - 409 (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 ARG 401 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I TYR* 3.7 17.4 - - - -
47I ASP* 2.7 43.2 + - - -
66I LYS* 4.7 3.6 - - - +
275I GLY 3.1 14.4 + - - +
318I GLU* 5.8 1.5 + - - -
393I PHE* 3.4 41.9 - - + -
394I PHE 3.3 5.8 - - - +
395I PHE* 3.6 32.1 - - + -
399I GLY 3.4 1.9 + - - +
400I LYS* 1.3 73.9 - - - +
402I TYR* 1.3 68.3 + - - +
403I ALA* 5.4 1.4 - - - +
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Residues in contact with TYR 402 (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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274I GLU 4.8 11.2 - - - -
275I GLY 3.4 14.4 - - - -
282I GLU* 4.1 32.4 + - + -
283I ASN* 4.5 3.8 - - - -
284I VAL* 3.5 21.5 - - + +
310I THR* 3.6 32.6 - - + +
312I GLN* 5.3 6.9 - - + +
314I LEU* 3.7 25.6 - - + -
392I LEU 3.7 1.0 - - - +
394I PHE* 2.6 44.6 + - - +
396I SER* 5.1 2.9 - - - -
400I LYS* 3.7 45.4 + - + +
401I ARG* 1.3 78.3 - - - +
403I ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 403 (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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46I TYR* 6.1 2.5 - - + -
275I GLY 3.5 7.1 + - - -
276I THR* 4.1 15.2 - - - +
277I VAL* 3.5 32.5 + - + +
283I ASN* 6.1 0.5 - - - +
284I VAL* 4.6 5.9 + - - +
391I LEU* 5.2 5.6 - - + -
392I LEU 3.4 5.2 - - - +
393I PHE* 3.5 30.3 - - + -
401I ARG* 4.2 2.2 - - + +
402I TYR* 1.3 71.4 - - - +
404I SER* 1.3 61.9 + - - +
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Residues in contact with SER 404 (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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277I VAL* 4.5 3.4 - - - -
284I VAL* 3.5 33.7 - - - -
285I THR* 4.4 0.4 - - - -
286I THR* 2.6 40.0 + - - +
391I LEU* 3.3 6.3 - - - -
392I LEU* 2.5 45.6 + - - +
394I PHE* 3.8 6.2 - - - -
402I TYR 4.0 0.4 + - - -
403I ALA* 1.3 74.3 - - - +
405I GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 405 (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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68I HIS* 2.8 39.5 + - + +
70I PHE* 3.6 29.5 - - + -
71I SER* 2.7 44.4 + - - -
277I VAL* 4.4 12.7 - - + +
286I THR* 3.1 20.2 + - - +
390I GLY 3.3 6.5 - - - +
391I LEU* 4.0 5.1 - - + +
404I SER* 1.3 73.1 - - - +
406I ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 406 (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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70I PHE* 3.5 5.5 - - - -
286I THR* 4.0 7.0 - - - +
287I GLU 3.7 5.8 - - - -
288I LEU* 3.3 52.0 - - + +
302I ILE* 4.8 7.4 - - + -
304I VAL* 3.9 19.1 - - + -
319I TYR* 3.7 29.2 - - + -
388I ILE* 5.2 4.0 - - + -
389I GLY* 3.4 1.2 - - - -
390I GLY 2.7 44.6 + - - +
392I LEU* 3.9 24.5 - - + -
404I SER 3.8 0.4 + - - -
405I GLU* 1.3 75.4 - - - +
407I GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 407 (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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266A LYS* 5.1 9.0 + - - +
41I ARG* 4.1 5.6 - - - -
70I PHE* 4.0 7.2 - - - -
288I LEU* 3.7 17.3 + - - +
388I ILE* 3.1 20.2 - - - -
389I GLY* 4.0 1.6 - - - -
406I ILE* 1.3 82.7 - - - +
408I GLY* 1.3 57.9 + - - -
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Residues in contact with GLY 408 (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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266A LYS* 5.8 4.0 - - - -
41I ARG* 3.7 2.9 - - - +
288I LEU* 3.7 10.9 - - - +
387I GLN* 3.4 18.6 - - - -
388I ILE* 2.7 31.1 + - - +
407I GLY* 1.3 75.1 - - - -
409I PRO* 1.3 76.2 - - - +
410I VAL 3.5 0.2 + - - -
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Residues in contact with PRO 409 (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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266A LYS* 5.8 5.4 - - - +
180B GLY 3.5 28.2 - - - +
181B GLN* 4.1 25.6 - - + +
182B LEU 5.1 1.8 - - - +
288I LEU* 4.2 6.4 - - + +
290I GLY* 4.7 4.9 + - - -
291I GLY 4.2 8.0 + - - -
386I SER 3.4 14.1 - - - +
387I GLN* 3.8 15.7 - - + +
408I GLY* 1.3 84.1 - - - +
410I VAL* 1.3 63.6 + - - +
411I ILE* 4.8 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