Contacts of the strand formed by residues 675 - 680 (chain A) in PDB entry 5FWW
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 ARG 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A PHE* 3.4 6.1 - - - +
670A ASP 2.9 28.1 + - - +
673A ASP* 3.1 35.1 + - + -
674A ASN* 1.3 74.7 - - - +
676A ILE* 1.3 63.8 + - - +
677A TYR* 4.1 18.2 - - + -
688A ARG* 3.6 35.4 - - + +
689A ALA* 3.2 28.8 - - - +
690A PHE* 3.6 29.2 - - + +
691A MET 4.9 0.2 - - - +
695A ALA* 3.7 22.2 + - - +
697A GLU* 2.8 27.7 + - - -
882A PHE* 4.0 2.2 - - - -
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Residues in contact with ILE 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A LEU* 3.6 18.6 - - + -
642A ILE* 4.9 11.2 - - + -
656A ILE* 3.9 36.6 - - + -
658A LEU* 4.8 6.3 - - + -
667A LEU* 5.2 5.4 - - + -
668A ASP 3.7 5.4 - - - +
669A PHE* 4.4 4.3 - - + -
675A ARG* 1.3 76.3 - - - +
677A TYR* 1.3 64.0 + - - +
678A TRP* 3.4 20.6 - - + -
688A ARG* 3.3 4.7 - - - +
689A ALA 2.9 40.7 + - - +
690A PHE 4.5 4.5 - - - +
691A MET* 3.6 27.6 - - - -
882A PHE* 4.1 4.9 - - + -
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Residues in contact with TYR 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A LEU* 3.5 4.9 - - - +
668A ASP 2.8 33.9 + - - +
669A PHE* 4.1 5.4 - - - -
670A ASP* 3.8 26.0 + - + -
673A ASP* 4.8 1.0 + - - -
675A ARG* 4.1 16.7 - - + -
676A ILE* 1.3 78.8 - - - +
678A TRP* 1.3 65.4 + - - +
686A ILE* 5.6 0.4 - - + -
687A SER 3.5 8.3 - - - +
688A ARG* 3.3 48.8 + - + -
699A VAL* 5.1 1.1 - - + -
710A MET* 3.3 19.7 - - + -
712A VAL* 3.7 16.8 - - + -
719A LEU* 4.0 19.1 - - + -
734A LEU* 3.5 41.0 - - + +
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Residues in contact with TRP 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A ILE* 3.6 23.6 - - + -
658A LEU* 3.6 24.7 - - + -
661A VAL* 4.0 20.5 - - + +
664A ALA* 4.0 22.7 - - + -
666A ALA 3.4 15.3 - - - +
667A LEU* 3.9 2.5 - - + -
676A ILE* 3.4 36.6 - - + -
677A TYR* 1.3 78.4 - - - +
679A THR* 1.3 69.9 + - - +
680A ASP* 4.7 8.1 + - + +
686A ILE* 3.6 1.4 - - - +
687A SER* 2.9 54.8 + - - -
688A ARG* 3.7 6.1 - - - -
689A ALA* 3.7 12.8 - - + -
696A LEU* 3.6 31.0 - - + -
710A MET* 3.5 4.4 - - - +
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Residues in contact with THR 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ALA* 3.5 3.6 - - - -
665A SER* 2.9 29.5 + - - -
666A ALA* 3.0 22.6 + - + +
678A TRP* 1.3 76.7 - - - +
680A ASP* 1.3 60.5 + - - +
681A ILE 4.0 0.4 - - - -
685A THR 3.5 6.7 - - - -
686A ILE* 3.9 17.0 - - + -
707A PRO* 2.8 35.6 + - + +
710A MET* 3.4 37.7 - - + -
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Residues in contact with ASP 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A VAL* 4.0 10.6 - - - +
662A LYS 3.4 19.4 + - - -
663A GLU 3.3 23.2 + - - +
664A ALA* 4.4 0.7 - - - +
678A TRP* 4.2 10.2 + - + +
679A THR* 1.3 72.0 - - - +
681A ILE* 1.3 54.3 + - - +
682A SER* 3.2 7.3 + - - -
683A LEU* 3.1 33.3 + - + +
684A LYS* 2.7 30.1 + - - -
685A THR* 2.8 33.6 + - - +
687A SER* 5.5 2.0 - - - +
707A PRO* 4.6 2.8 - - - +
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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