Contacts of the strand formed by residues 399 - 404 (chain D) in PDB entry 4JF7
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 SER 399 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PHE* 5.6 3.1 - - - -
395D MET* 3.5 3.8 - - - +
396D TYR* 2.8 36.8 + - - +
398D ASP* 1.3 80.8 + - - +
400D VAL* 1.3 62.8 + - - +
401D TYR* 3.9 16.4 + - - -
417D LYS* 3.3 34.7 + - - +
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Residues in contact with VAL 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D VAL* 4.8 3.4 - - + -
297D TYR* 3.8 38.6 - - + -
302D LEU* 4.4 11.9 - - + -
362D ILE* 5.3 0.2 - - + -
393D LEU* 4.1 14.8 - - + -
394D TYR 3.3 10.8 - - - +
395D MET* 4.0 10.1 - - + -
398D ASP 4.8 0.2 - - - +
399D SER* 1.3 72.2 - - - +
401D TYR* 1.3 74.4 + - - +
417D LYS* 3.9 1.7 - - - +
418D VAL* 2.8 50.7 + - + +
420D ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE* 4.0 18.4 - + - -
393D LEU* 3.3 9.5 - - - +
394D TYR* 2.9 38.6 + - + -
396D TYR* 3.6 29.6 - + + -
399D SER* 4.0 14.4 - - - -
400D VAL* 1.3 78.9 - - - +
402D TYR* 1.3 60.2 + - - +
415D LEU* 5.1 2.9 - - + -
416D TYR 3.1 23.3 - - - -
417D LYS* 3.6 32.4 - - + +
418D VAL* 4.1 3.1 - - - -
435D VAL* 4.2 11.2 - - + -
468D LEU* 3.6 24.0 - - + -
471D ASN* 4.3 2.6 + - - -
472D PRO* 3.5 22.4 - - + +
473D SER* 4.5 1.0 + - - -
478D PHE* 3.5 15.2 - - - -
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Residues in contact with TYR 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D PRO* 4.0 23.2 - - + +
305D ILE 4.4 4.3 + - - -
360D SER* 2.7 25.5 + - - -
361D GLY 4.7 2.0 - - - -
362D ILE* 5.3 0.4 - - + -
380D PHE* 3.5 34.5 - + - -
385D VAL* 4.6 1.3 - - + -
389D ALA 3.8 10.6 + - - -
390D GLU 4.3 0.5 + - - -
391D GLY* 4.2 1.0 - - - -
392D ARG 3.3 10.3 - - - -
393D LEU* 4.0 13.7 - - + -
394D TYR* 4.6 2.0 - - - -
401D TYR* 1.3 75.0 - - - +
403D TYR* 1.3 77.6 + - - +
404D GLN* 3.5 25.7 - - + +
415D LEU* 3.4 5.7 - - - +
416D TYR* 3.0 56.6 + + + +
418D VAL* 3.5 19.5 - - + +
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Residues in contact with TYR 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D GLY* 3.1 5.6 - - - -
392D ARG* 2.8 34.0 + - + +
394D TYR* 3.6 23.8 - - + +
402D TYR* 1.3 82.6 - - - +
404D GLN* 1.3 68.9 + - - +
405D ARG* 3.5 25.9 - - - -
406D SER 4.5 1.8 + - - -
413D THR* 4.4 6.5 - - + -
414D MET 3.4 23.8 - - - -
415D LEU* 3.7 14.1 - - + -
462D VAL 4.2 2.1 + - - -
463D TYR* 3.7 31.0 - + - -
464D ALA* 2.9 42.0 + - - +
465D ASP* 3.4 25.4 - - + -
466D ALA 4.3 0.7 - - - -
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Residues in contact with GLN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D SER* 3.3 20.7 + - - +
385D VAL* 3.3 11.4 - - - +
386D LEU* 3.0 42.5 + - - +
387D MET 3.3 9.6 + - - -
389D ALA* 4.5 2.7 - - + -
390D GLU 3.9 4.7 - - - +
402D TYR* 3.5 22.8 + - + +
403D TYR* 1.3 82.9 - - - +
405D ARG* 1.3 76.8 + - - +
406D SER 3.4 1.0 + - - -
414D MET* 3.0 28.2 + - + +
416D TYR* 2.8 34.7 + - + -
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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