Contacts of the strand formed by residues 681 - 689 (chain C) in PDB entry 3FBY
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 SER 681 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C THR 4.4 2.8 + - - +
271C ASP* 2.7 42.0 + - - -
272C LEU* 3.6 12.7 - - - +
296C PRO* 3.7 1.7 - - - +
585C THR* 3.8 8.5 - - - +
586C PHE 3.5 3.6 - - - -
587C HIS* 2.6 28.8 + - - +
680C LYS* 1.3 83.0 - - - +
682C TYR* 1.3 65.5 + - - +
701C GLU* 4.4 0.2 - - - -
702C GLY 4.1 9.7 + - - -
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Residues in contact with TYR 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 3.7 3.4 - - - -
585C THR* 3.3 4.9 - - - +
586C PHE* 2.8 61.0 + + + +
614C TRP* 3.7 27.1 - + + -
672C ARG* 6.2 0.4 - - - -
675C GLY 4.6 1.0 + - - -
676C TRP* 3.7 19.1 - - + -
677C LYS* 3.0 32.7 + - - +
680C LYS* 3.4 32.1 - - + +
681C SER* 1.3 74.3 - - - +
683C ARG* 1.3 60.3 + - - +
684C TRP 4.1 0.2 + - - -
699C PHE* 4.6 10.8 - + + -
700C TYR 3.2 8.5 - - - +
701C GLU* 3.8 40.2 + - + -
706C VAL* 5.1 6.1 - - + -
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Residues in contact with ARG 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 3.9 24.2 - - + -
272C LEU* 3.5 19.3 - - + +
583C GLU* 3.2 43.6 + - + +
584C GLY* 3.2 10.2 - - - +
585C THR* 2.8 41.7 + - - +
682C TYR* 1.3 73.3 - - - +
684C TRP* 1.3 69.5 + - - +
685C PHE* 6.1 0.4 - - + -
698C ARG 3.9 0.7 - - - +
699C PHE* 3.3 4.5 - - - -
700C TYR* 2.5 46.5 + - + +
735C ALA 3.4 1.4 + - - -
736C ASN* 2.8 47.4 + - - +
738C ARG* 4.1 4.4 - - - +
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Residues in contact with TRP 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C PHE* 3.5 48.6 + + - -
583C GLU* 3.1 27.3 - - - +
584C GLY* 2.8 53.8 + - - +
585C THR 3.7 10.5 - - - -
586C PHE* 3.9 17.7 - - + -
599C PHE* 3.6 47.9 - + + -
682C TYR 4.1 1.0 + - - -
683C ARG* 1.3 77.8 - - - +
685C PHE* 1.3 63.3 + - - +
686C LEU 4.2 0.4 - - - -
697C VAL* 5.4 0.2 - - + -
698C ARG 3.6 4.7 - - - +
699C PHE* 3.6 29.6 - + + -
700C TYR* 5.8 0.2 - - - -
724C VAL* 4.9 1.3 - - + -
734C TRP* 3.8 28.3 - + - -
737C LEU* 3.7 13.7 - - + -
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Residues in contact with PHE 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C ASP* 3.9 22.4 - - + -
582C PHE 3.5 2.2 - - - -
583C GLU* 4.0 30.3 - - + -
683C ARG* 4.2 0.4 + - + -
684C TRP* 1.3 76.1 - - - +
686C LEU* 1.3 67.7 + - - +
687C GLN* 3.6 33.9 - - + -
696C ARG 3.8 1.2 - - - +
697C VAL* 3.5 2.7 - - - -
698C ARG* 2.9 73.2 + - + +
700C TYR* 5.2 7.9 - - + -
740C ARG* 4.9 2.9 - - - -
1002C SO4 3.9 32.1 - - - +
1003C SO4 5.9 0.2 - - - -
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Residues in contact with LEU 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL* 5.3 2.7 - - + +
581C ASP* 3.4 6.4 - - - +
582C PHE* 2.7 61.2 + - + +
599C PHE* 3.8 19.1 - - + -
601C PHE* 3.6 61.9 - - + -
685C PHE* 1.3 76.2 - - - +
687C GLN* 1.3 84.2 + - - +
688C HIS* 4.7 5.4 - - + -
695C ILE* 4.7 2.0 - - + -
696C ARG 3.4 10.5 - - - +
697C VAL* 4.4 9.4 - - + +
722C LEU* 4.7 1.3 - - + -
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Residues in contact with GLN 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL 3.7 3.6 - - - -
581C ASP* 3.6 12.6 + - - +
685C PHE* 3.6 30.5 - - + -
686C LEU* 1.3 82.2 - - - +
688C HIS* 1.3 62.1 + - - +
689C ARG* 3.9 19.5 - - - +
694C TYR* 3.6 13.9 - - + +
695C ILE* 3.3 5.7 - - - -
696C ARG* 2.8 56.0 + - - +
698C ARG* 3.9 11.2 + - - +
746C PRO* 4.3 4.4 - - - +
1003C SO4 3.7 32.2 + - - -
1F NAG 4.2 4.8 + - - -
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Residues in contact with HIS 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C ASN 4.0 2.5 - - - -
579C GLY* 3.2 1.6 - - - -
580C VAL* 2.7 59.3 + - + -
601C PHE* 3.6 32.5 - + + -
602C GLY* 4.6 9.6 - - - -
610C TYR* 4.1 7.4 - + - -
686C LEU* 4.7 4.5 - - + -
687C GLN* 1.3 75.4 - - - +
689C ARG* 1.3 63.7 + - - +
690C PRO* 3.6 37.3 - - + +
693C GLY* 5.7 1.6 - - - -
694C TYR 3.3 11.2 + - - -
695C ILE* 3.5 14.4 - - + +
714C ASP 5.7 1.1 - - - -
717C MET 3.8 20.3 + - - -
719C GLY* 3.8 9.8 + - - -
720C GLY 5.6 0.4 - - - -
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Residues in contact with ARG 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C GLY* 4.2 1.3 - - - -
580C VAL 2.9 28.7 + - - -
581C ASP* 2.7 22.0 + - - -
687C GLN* 3.9 17.5 - - - +
688C HIS* 1.3 84.1 + - - +
690C PRO* 1.3 56.9 - - - +
691C GLN* 3.1 14.7 + - - +
692C VAL* 3.3 10.2 + - + +
693C GLY 2.8 26.0 + - - -
694C TYR* 2.8 31.4 + - + -
742C ASN* 3.2 40.3 + - - -
743C ASP 3.8 15.0 - - - -
744C THR 3.2 17.2 + - - -
745C ILE* 4.4 2.0 - - + -
746C PRO* 4.1 19.9 - - + +
1F NAG 3.5 11.1 + - - -
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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