Contacts of the helix formed by residues 521 - 525 (chain B) in PDB entry 5M64
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 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A PRO* 4.8 12.6 - - + -
996A TYR* 2.5 25.1 + - - -
1000A MET* 4.8 0.7 - - - -
393B ASN* 4.5 11.9 - - - +
395B ASP* 5.0 9.0 - - - +
396B ALA* 3.6 38.1 - - + +
397B THR* 5.9 2.5 - - + +
516B THR 5.8 3.1 - - - +
519B LYS 5.2 1.8 - - - +
520B LEU* 1.3 85.0 - - - +
522B PRO* 1.3 67.6 - - + +
523B GLU* 3.1 22.9 - - + +
524B SER* 2.5 20.6 + - - +
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Residues in contact with PRO 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A VAL* 4.4 11.4 - - + -
958A PRO* 3.8 26.5 - - + +
959A VAL* 5.8 2.2 - - - -
965A THR 3.2 28.5 - - - +
966A LEU* 4.6 7.9 - - + +
967A PRO* 4.0 7.5 - - - +
996A TYR* 3.4 21.1 + - + +
997A PHE* 4.8 1.6 - - + -
1000A MET* 5.6 3.6 - - + -
521B LEU* 1.3 90.9 - - + +
523B GLU* 1.3 70.8 + - - +
524B SER 3.1 2.2 + - - -
525B TRP* 3.2 21.5 + - - +
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A VAL 5.0 1.1 - - - +
960A MET* 3.2 35.0 - - + +
967A PRO* 5.5 3.8 - - - +
393B ASN* 6.0 0.5 + - - -
396B ALA* 5.6 1.3 - - - +
397B THR* 3.2 21.1 + - + +
398B GLN* 3.2 27.7 - - + +
521B LEU* 3.1 24.4 - - + +
522B PRO* 1.3 86.1 - - - +
524B SER* 1.3 55.9 + - - +
525B TRP* 3.1 3.4 + - - +
527B PHE* 3.1 29.1 - - - -
670B VAL* 5.1 11.4 - - + +
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Residues in contact with SER 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A TYR* 2.4 33.5 + - - -
397B THR* 4.0 13.3 + - - +
520B LEU* 4.7 9.4 - - - +
521B LEU* 2.5 15.2 + - - +
523B GLU* 1.3 76.2 - - - +
525B TRP* 1.3 62.1 + - - +
526B GLY 3.1 3.6 + - - -
527B PHE* 3.3 11.8 + - - -
528B LEU* 3.3 42.9 + - - +
530B PRO* 5.0 0.7 - - - +
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Residues in contact with TRP 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A LEU* 3.8 21.1 - - + -
967A PRO* 3.8 22.9 - - + -
968A SER* 5.5 1.0 - - - -
992A PRO* 3.7 24.0 - - + -
993A GLN* 3.6 13.9 - - - -
996A TYR* 3.6 47.1 + + + -
522B PRO 3.2 15.2 + - - +
523B GLU 3.1 3.4 - - - +
524B SER* 1.3 74.1 - - - +
526B GLY* 1.3 65.0 + - - +
527B PHE* 3.2 7.8 + - - -
651B ARG* 4.3 10.3 - - - +
669B GLN* 3.0 32.2 - - - +
674B ILE* 6.1 3.6 - - + +
676B VAL* 3.6 27.4 - - + +
690B GLU* 5.9 3.2 + - - +
693B PRO* 5.7 3.6 - - + -
696B ILE* 3.6 26.0 - - + +
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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
------------------------------------------------------------
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