Contacts of the strand formed by residues 681 - 689 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A THR 4.3 5.6 - - - -
271A ASP* 3.2 39.3 + - - -
272A LEU* 3.3 15.5 - - - +
585A THR* 3.3 14.9 - - - +
586A PHE 3.5 3.4 - - - -
587A HIS* 3.3 18.7 + - - -
680A LYS* 1.3 82.9 - - - +
682A TYR* 1.3 62.3 + - - +
701A GLU* 4.3 1.2 - - - -
702A GLY* 3.9 9.7 + - - -
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Residues in contact with TYR 682 (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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272A LEU* 3.9 3.1 - - - -
585A THR* 3.2 3.7 - - - -
586A PHE* 2.7 53.7 + + + +
614A TRP* 3.4 39.5 - + + -
675A GLY 4.3 1.9 + - - -
676A TRP* 3.5 18.4 - - + -
677A LYS* 2.8 39.8 + - - +
680A LYS* 3.8 31.0 - - + +
681A SER* 1.3 74.9 + - - +
683A ARG* 1.3 60.7 + - - +
684A TRP* 4.9 0.4 - - - -
699A PHE* 5.0 7.0 - + + -
700A TYR 3.3 8.5 - - - +
701A GLU* 3.4 40.2 - - + -
706A VAL* 5.1 4.9 - - + -
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Residues in contact with ARG 683 (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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257A VAL* 3.8 32.5 - - + +
272A LEU* 3.7 12.9 + - + +
583A GLU* 3.3 37.7 + - + +
584A GLY* 3.4 11.0 + - - +
585A THR* 2.9 30.3 + - - +
682A TYR* 1.3 73.7 - - - +
684A TRP* 1.3 66.5 + - - +
685A PHE* 6.1 0.7 - - + -
699A PHE* 3.4 4.5 - - - -
700A TYR* 2.8 47.6 + - + -
735A ALA 3.5 1.6 + - - -
736A ASN* 2.6 51.3 + - - +
738A ARG* 4.4 3.2 - - - +
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Residues in contact with TRP 684 (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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582A PHE* 3.5 47.1 + + - -
583A GLU* 3.0 28.2 - - - +
584A GLY* 2.8 52.8 + - - +
585A THR 3.9 3.4 - - - -
586A PHE* 3.9 22.2 - - + -
598A GLY 6.0 0.2 - - - -
599A PHE* 3.5 47.2 - + + -
682A TYR 4.9 0.2 - - - -
683A ARG* 1.3 78.6 - - - +
685A PHE* 1.3 64.8 + - - +
686A LEU 4.1 0.2 - - - -
698A ARG 3.3 4.9 - - - +
699A PHE* 3.5 28.3 - + + -
700A TYR* 5.5 0.2 - - - -
724A VAL* 4.7 0.9 - - + -
734A TRP* 3.7 32.8 - + - -
737A LEU* 3.8 9.6 - - + -
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Residues in contact with PHE 685 (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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581A ASP* 4.1 23.1 - - + -
582A PHE 3.7 2.2 - - - -
583A GLU* 3.6 32.3 - - + -
683A ARG* 6.1 1.1 - - + -
684A TRP* 1.3 75.5 - - - +
686A LEU* 1.3 67.4 + - - +
687A GLN* 3.7 27.6 - - + -
696A ARG 3.6 1.4 - - - +
697A VAL* 3.3 3.8 - - - -
698A ARG* 2.8 77.2 + - + +
700A TYR* 4.8 10.8 - + + -
740A ARG* 4.3 4.5 - - - -
1003A SO4 5.3 1.3 - - - -
1D NAG 5.8 0.9 - - + -
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Residues in contact with LEU 686 (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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580A VAL* 5.2 2.7 - - + +
581A ASP* 3.7 3.1 - - - -
582A PHE* 2.8 50.6 + - + +
599A PHE* 3.9 19.7 - - + -
601A PHE* 3.4 66.0 - - + -
684A TRP* 4.1 0.6 - - - -
685A PHE* 1.3 78.3 - - - +
687A GLN* 1.3 93.2 + - - +
688A HIS* 4.2 4.5 - - + +
695A ILE* 4.4 1.8 - - + -
696A ARG 3.4 3.8 - - - -
697A VAL* 3.9 15.0 - - + -
722A LEU* 4.3 2.0 - - + -
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Residues in contact with GLN 687 (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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580A VAL 3.9 3.6 - - - -
581A ASP* 3.6 14.5 + - - +
685A PHE* 3.7 21.6 - - + -
686A LEU* 1.3 82.1 - - - +
688A HIS* 1.3 60.2 + - - +
689A ARG* 3.9 8.6 - - - +
694A TYR* 3.6 14.3 - - + +
695A ILE* 3.3 6.4 - - - -
696A ARG* 2.8 48.9 + - - +
698A ARG* 3.3 22.9 + - - -
746A PRO* 3.6 9.5 - - - +
1003A SO4 3.1 24.7 + - - -
1D NAG 3.1 15.8 + - - -
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Residues in contact with HIS 688 (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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578A ASN 4.5 4.5 - - - -
579A GLY* 3.3 1.2 - - - -
580A VAL* 3.0 39.0 + - + -
601A PHE* 3.8 29.4 - + + -
602A GLY* 4.9 6.2 - - - -
610A TYR* 4.2 15.8 - + - -
686A LEU* 4.2 3.6 - - + +
687A GLN* 1.3 74.4 - - - +
689A ARG* 1.3 78.0 + - - +
690A PRO* 3.7 39.2 - - + +
694A TYR 3.2 13.2 + - - -
695A ILE* 3.7 19.3 - - + +
714A ASP 5.1 4.7 - - - -
717A MET 3.7 14.5 + - - -
719A GLY* 4.0 6.7 + - - -
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Residues in contact with ARG 689 (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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579A GLY* 4.0 3.1 - - - -
580A VAL 3.1 17.4 + - - -
581A ASP* 3.0 18.6 + - - -
687A GLN* 3.9 7.0 - - - +
688A HIS* 1.3 104.4 + - - +
690A PRO* 1.3 69.5 - - - +
691A GLN* 3.1 6.7 - - - +
692A VAL* 3.0 4.5 + - + -
693A GLY 3.0 17.3 + - - -
694A TYR* 2.9 31.5 + - + -
742A ASN* 2.8 46.9 + - - +
743A ASP* 4.0 11.9 - - - +
744A THR 3.1 15.3 + - - -
745A ILE* 3.9 15.5 - - + -
746A PRO* 3.8 21.7 - - + +
1D NAG 3.5 13.3 + - - -
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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