Contacts of the strand formed by residues 642 - 646 (chain F) in PDB entry 6MZL
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 VAL 642 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601F VAL* 3.7 23.3 - - + -
611F LEU* 5.1 2.9 - - + -
623F PHE* 4.5 15.9 - - + -
633F THR* 4.6 1.8 - - - +
634F ARG 3.3 10.5 - - - +
635F PHE* 3.6 29.2 - - + -
636F HIS 4.7 0.4 - - - +
640F ASN 4.1 2.9 + - - +
641F TYR* 1.3 78.8 - - - +
643F ALA* 1.3 64.1 + - - +
644F THR* 4.6 2.2 - - - +
653F LEU* 3.5 11.2 - - - +
654F TRP* 3.2 54.3 + - + +
655F ASP 5.5 0.7 - - - +
677F PHE* 4.6 2.5 - - - -
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Residues in contact with ALA 643 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632F CYS* 6.3 0.2 - - - -
633F THR* 3.2 25.8 + - - -
634F ARG 3.1 10.4 + - - +
642F VAL* 1.3 75.4 - - - +
644F THR* 1.3 68.2 + - - +
645F GLY 4.4 0.2 - - - -
651F VAL* 4.6 3.8 - - + -
652F ARG 3.8 2.5 - - - -
653F LEU* 3.7 13.5 - - + -
675F LEU* 3.7 28.0 - - + -
677F PHE* 3.6 23.9 - - + -
684F LEU* 5.5 0.2 - - + -
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Residues in contact with THR 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609F ALA* 4.2 15.4 - - + +
623F PHE 6.0 0.4 - - - +
626F HIS* 3.3 27.0 + - + +
630F VAL* 3.7 29.6 - - + -
632F CYS 3.4 3.6 - - - +
633F THR* 3.9 6.8 + - - -
642F VAL* 4.6 1.7 - - - +
643F ALA* 1.3 79.3 + - - +
645F GLY* 1.3 61.8 + - - +
651F VAL* 3.5 6.2 - - - -
652F ARG 3.1 28.1 + - - +
654F TRP* 3.1 32.2 + - - +
675F LEU* 5.1 0.4 - - - -
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Residues in contact with GLY 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630F VAL* 3.7 3.6 - - - +
631F ASN* 2.7 29.3 + - - -
632F CYS* 2.7 38.8 + - - +
644F THR* 1.3 73.9 - - - +
646F SER* 1.3 56.3 + - - -
650F THR 3.9 0.7 - - - -
651F VAL* 4.9 3.1 - - - -
672F ILE* 3.9 16.6 - - - -
675F LEU* 4.9 0.8 - - - +
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Residues in contact with SER 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626F HIS* 3.5 22.7 - - - +
628F ALA 3.4 11.8 + - - -
629F ASP 2.7 22.8 + - - -
630F VAL* 3.8 6.5 - - - -
631F ASN* 3.1 15.1 + - - +
645F GLY* 1.3 75.5 - - - -
647F ALA* 1.3 71.4 + - - +
648F ASP* 3.2 19.9 + - - -
649F ARG 3.6 8.3 + - - -
650F THR 3.8 6.1 + - - -
672F ILE* 3.7 12.9 + - - +
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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