Contacts of the strand formed by residues 464 - 472 (chain B) in PDB entry 2H5G
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 LEU 464 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B ARG* 3.7 0.9 - - - -
460B ILE* 2.8 54.1 + - + +
461B ALA* 3.0 16.2 + - + +
463B ASN* 1.3 78.4 - - - +
465B GLU* 1.3 57.0 + - - +
764B LEU* 3.7 38.1 - - + -
765B ARG 3.6 0.9 - - - +
766B GLY* 3.5 23.8 - - - -
769B HIS* 3.9 38.4 - - + +
774B PHE* 4.3 13.9 - - + -
782B TYR* 5.3 1.8 - - + -
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B THR 3.7 1.4 - - - +
459B ARG* 2.8 59.2 + - - +
463B ASN* 4.7 7.7 + - - -
464B LEU* 1.3 80.3 - - - +
466B LEU* 1.3 61.1 + - - +
763B LEU 3.8 0.9 - - - +
764B LEU* 3.5 4.9 - - - +
765B ARG* 3.0 44.9 + - + +
787B LEU* 3.4 17.5 - - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG* 5.9 2.0 - - + +
457B ARG* 3.4 5.7 - - - +
458B THR* 2.7 48.2 + - - +
460B ILE* 3.7 28.7 - - + +
465B GLU* 1.3 75.4 - - - +
467B GLU* 1.3 66.0 + - - +
762B TRP* 3.7 44.2 - - + -
763B LEU 3.3 23.6 - - - +
764B LEU* 3.9 13.7 - - + -
765B ARG* 6.0 0.2 - - - -
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B VAL* 3.9 23.3 - - + +
456B ARG 3.2 12.6 - - - +
457B ARG* 4.6 9.1 + - + +
466B LEU* 1.3 81.9 - - - +
468B GLN* 1.3 59.5 + - - +
469B VAL* 3.8 17.6 - - + +
761B LYS 3.9 0.3 - - - +
762B TRP* 3.5 1.9 - - - -
763B LEU* 2.8 48.1 + - + +
765B ARG* 2.9 38.9 + - - +
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B VAL* 3.6 0.9 - - - -
455B LEU* 2.7 49.4 + - + +
456B ARG* 2.9 36.3 + - + +
467B GLU* 1.3 72.6 - - - +
469B VAL* 1.3 62.5 + - - +
760B THR* 3.2 33.4 + - - +
761B LYS 3.4 9.2 - - - +
762B TRP* 3.4 45.5 - - + +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLY* 4.2 12.1 - - - +
453B ARG 3.3 11.7 - - - +
454B VAL* 4.2 11.0 - - + -
455B LEU* 4.5 2.5 - - - +
467B GLU* 3.8 32.3 - - + +
468B GLN* 1.3 79.6 - - - +
470B THR* 1.3 69.7 + - - +
471B VAL* 4.3 11.4 - - + -
760B THR* 3.1 6.7 - - - -
761B LYS* 2.8 42.6 + - + +
763B LEU* 4.0 16.8 - - + -
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Residues in contact with THR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B SER 2.7 28.0 + - - +
451B VAL* 3.6 1.1 - - - +
452B GLY* 3.0 31.5 + - - -
453B ARG* 3.1 27.2 + - + +
455B LEU* 3.9 26.0 - - + -
469B VAL* 1.3 74.7 - - - +
471B VAL* 1.3 65.8 + - - +
758B LEU* 4.3 16.2 - - + -
759B THR 3.3 12.3 - - - +
760B THR* 4.3 0.9 - - + +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B VAL* 5.1 1.6 - - - -
469B VAL* 4.3 6.3 - - + -
470B THR* 1.3 80.4 - - - +
472B PRO* 1.4 75.7 - - + +
758B LEU* 3.5 9.8 - - - -
759B THR* 2.9 50.7 + - + +
760B THR 4.0 13.0 - - - +
761B LYS* 4.0 37.5 - - + +
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Residues in contact with PRO 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ALA* 3.9 17.7 - - + -
451B VAL* 4.4 11.4 - - + -
471B VAL* 1.4 99.4 - - + +
473B ILE* 1.3 64.1 + - - +
474B GLY* 3.4 6.6 + - - +
497B SER 3.4 19.7 - - - +
498B GLY 3.2 27.8 - - - +
499B ASN* 3.4 11.4 - - - +
757B LEU 4.1 3.6 - - - +
758B LEU* 4.2 0.6 - - + -
759B THR* 3.8 2.9 - - - +
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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