Contacts of the strand formed by residues 649 - 652 (chain F) in PDB entry 6IWQ
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 TRP 649 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537F ILE* 3.8 16.4 - - + -
538F ARG 3.3 22.4 - - - +
539F GLY 4.2 4.0 - - - -
540F PHE* 4.1 1.8 - - - +
546F ILE* 3.5 27.8 - - + -
559F LEU* 4.1 11.7 - - + -
610F TYR* 4.4 6.2 + - - -
615F HIS* 2.6 38.4 + - - +
617F PHE* 3.9 30.1 - + + -
626F LEU* 3.3 40.2 + - + +
627F ASP 4.2 9.2 - - - -
628F ARG* 3.5 52.7 - - + -
635F VAL* 4.5 2.5 - - + -
646F THR 3.9 2.0 + - - -
647F GLN 3.3 17.9 + - - -
648F LYS* 1.3 70.0 - - - +
650F GLU* 1.3 61.3 - - - +
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Residues in contact with GLU 650 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537F ILE* 3.6 5.2 - - - +
538F ARG* 3.1 51.2 + - + +
540F PHE* 4.3 22.3 - - + -
541F GLU* 4.1 13.7 + - - -
610F TYR* 3.9 5.6 - - - +
615F HIS* 4.9 10.2 - - + +
617F PHE* 5.2 0.7 - - - -
649F TRP* 1.3 78.1 - - - +
651F MET* 1.3 61.1 + - - +
652F ASN* 3.3 31.1 + - - +
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Residues in contact with MET 651 (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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533F ASP* 3.9 24.1 - - - +
534F TRP* 3.5 7.0 - - - +
535F GLY 3.4 16.8 - - - +
536F GLU 3.1 11.9 - - - +
537F ILE* 3.8 15.5 - - + -
571F PHE* 3.3 42.6 - - + +
572F ARG* 3.7 7.6 - - - +
573F ILE* 3.7 29.8 - - + -
579F LEU* 4.9 0.2 - - + -
610F TYR* 3.1 25.3 + - + +
617F PHE* 4.1 10.8 - - + -
650F GLU* 1.3 71.2 - - - +
652F ASN* 1.3 67.8 + - - +
653F ASN* 5.1 0.3 + - - -
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Residues in contact with ASN 652 (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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534F TRP 3.7 2.0 - - - -
535F GLY* 3.0 0.3 - - - -
536F GLU* 2.8 63.2 + - - +
538F ARG* 4.1 7.9 - - - +
650F GLU* 3.3 42.0 + - - +
651F MET* 1.3 82.9 - - - +
653F ASN* 1.3 68.4 + - - +
654F ILE* 3.1 1.1 + - + -
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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