Contacts of the strand formed by residues 474 - 480 (chain x) in PDB entry 5GJQ
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 ALA 474 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327x MET* 4.0 15.3 - - + -
329x ARG* 3.1 25.7 + - - +
348x PHE* 4.0 15.0 - - + -
422x VAL* 4.5 1.6 - - + -
423x LEU 3.4 10.1 - - - +
465x LEU* 2.8 22.5 + - + +
473x ILE* 1.3 76.2 - - - +
475x TYR* 1.3 60.2 + - - +
477x LEU* 3.6 27.6 - - + -
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Residues in contact with TYR 475 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198x ASP* 3.0 24.0 + - - -
200x ASN* 3.5 34.8 + - + +
326x GLN* 3.8 4.0 + - + +
327x MET* 3.1 42.6 + - - +
329x ARG* 4.4 3.6 - - - -
330x PHE* 3.1 25.7 - + - -
423x LEU* 3.3 25.0 + - + +
425x HIS* 4.4 10.3 - - + +
435x TYR* 4.5 7.0 - + - -
473x ILE 4.3 4.7 - - - +
474x ALA* 1.3 75.6 - - - +
476x VAL* 1.3 79.9 + - + +
42y ARG* 4.0 8.0 + - - -
70y VAL* 4.4 1.6 - - - +
73y LEU* 3.3 38.4 - - + -
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Residues in contact with VAL 476 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200x ASN* 3.5 26.5 - - + +
203x TRP* 3.6 30.5 - - + -
273x GLN* 4.1 4.0 - - - +
324x THR* 3.8 15.0 - - + -
325x ILE 3.4 7.6 - - - +
326x GLN* 4.3 6.5 - - - -
422x VAL 3.6 1.6 - - - -
423x LEU* 3.1 36.1 + - + +
475x TYR* 1.3 101.3 - - + +
477x LEU* 1.3 81.7 + - - +
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Residues in contact with LEU 477 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285x LEU* 3.9 14.1 - - + -
324x THR* 3.7 1.6 - - - -
325x ILE* 3.2 31.0 + - + +
327x MET* 3.6 27.4 - - - -
348x PHE* 3.7 43.1 - - + -
419x LEU* 4.1 4.5 - - + -
421x ALA 3.5 4.3 - - - -
422x VAL* 4.2 9.4 - - + -
474x ALA* 3.6 26.7 - - + -
476x VAL* 1.3 93.6 - - - +
478x LEU* 1.3 60.7 + - - +
479x TYR* 3.8 18.4 - - + +
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Residues in contact with LEU 478 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121x CYS 4.4 2.2 - - - +
124x SER* 3.6 17.9 - - - +
125x VAL* 3.8 11.7 - - + -
203x TRP* 3.9 30.3 - - + -
246x PHE* 4.3 16.2 - - + -
322x TYR* 5.1 3.1 - - + -
323x LEU 3.6 3.6 - - - +
324x THR* 3.9 18.8 - - + +
419x LEU* 3.1 3.8 - - - +
420x GLN* 2.8 58.6 + - - +
421x ALA* 2.8 28.1 + - + +
477x LEU* 1.3 76.4 - - - +
479x TYR* 1.3 63.9 + - - +
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Residues in contact with TYR 479 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285x LEU* 4.2 3.1 - - + -
321x ALA 4.1 0.3 - - - +
322x TYR* 3.2 8.2 - - - +
323x LEU* 2.8 39.9 + - + +
325x ILE* 3.7 31.9 - - + -
348x PHE* 3.6 14.2 - - - +
349x PRO* 2.9 40.3 + - + +
350x LEU 4.5 0.7 - - - -
352x LEU* 4.1 24.2 - - + -
417x TYR* 3.9 24.0 - - + -
418x ASP 3.5 2.5 - - - -
419x LEU* 3.1 46.7 - - + -
420x GLN* 4.9 0.2 - - - -
477x LEU* 3.8 21.5 - - + -
478x LEU* 1.3 77.2 - - - +
480x GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 480 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321x ALA 3.8 2.5 - - - -
322x TYR* 3.7 9.4 - - - -
417x TYR* 3.5 5.0 - - - -
418x ASP 2.6 40.4 + - - +
420x GLN* 4.0 13.0 - - - +
478x LEU 4.0 0.8 + - - -
479x TYR* 1.3 74.8 - - - +
481x PRO* 1.4 79.8 - - - +
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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