Contacts of the strand formed by residues 681 - 689 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B THR 4.2 3.9 - - - +
271B ASP* 2.6 44.0 + - - -
272B LEU* 3.7 15.9 - - - +
296B PRO* 4.0 0.5 - - - +
585B THR* 3.8 3.5 - - - +
586B PHE 3.8 2.2 - - - -
587B HIS* 2.8 28.2 - - - +
680B LYS* 1.3 82.0 - - - +
682B TYR* 1.3 65.3 + - - +
701B GLU* 4.4 0.2 - - - -
702B GLY* 3.9 12.1 + - - -
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Residues in contact with TYR 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.7 3.1 - - - -
585B THR* 3.2 5.2 - - - +
586B PHE* 2.7 55.9 + + + +
588B VAL* 6.5 0.4 - - + -
614B TRP* 3.5 38.3 - + + -
672B ARG* 6.0 0.7 - - - -
675B GLY 4.6 0.9 + - - -
676B TRP* 3.7 18.1 - - + -
677B LYS* 2.8 46.7 + - - +
680B LYS* 3.3 29.1 - - + +
681B SER* 1.3 73.9 - - - +
683B ARG* 1.3 60.4 + - - +
699B PHE* 5.1 7.6 - + + -
700B TYR 3.3 7.6 - - - +
701B GLU* 3.4 40.4 - - + -
706B VAL* 5.1 4.5 - - + -
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Residues in contact with ARG 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 4.1 22.0 - - + -
272B LEU* 3.7 16.5 - - + +
583B GLU* 3.0 40.6 + - - +
584B GLY* 3.2 8.9 - - - +
585B THR* 2.6 47.3 + - - +
682B TYR* 1.3 74.3 - - - +
684B TRP* 1.3 63.9 + - - +
685B PHE* 3.8 17.4 - - + -
699B PHE* 3.3 6.4 - - - -
700B TYR* 2.8 43.7 + - + -
736B ASN* 2.9 44.9 + - - +
738B ARG* 4.5 6.1 - - - +
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Residues in contact with TRP 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PHE* 3.7 42.0 + + - -
583B GLU* 3.2 23.1 - - - +
584B GLY* 2.9 47.4 + - - +
585B THR 4.0 1.8 - - - -
586B PHE* 3.7 31.6 - - + -
598B GLY 6.0 0.2 - - - -
599B PHE* 3.3 51.9 - + + -
683B ARG* 1.3 75.8 - - - +
685B PHE* 1.3 66.3 + - - +
698B ARG 3.4 4.3 - - - -
699B PHE* 3.8 20.0 - + + -
724B VAL* 4.7 0.4 - - + -
734B TRP* 3.6 25.8 - + - -
737B LEU* 3.5 20.4 - - + -
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Residues in contact with PHE 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 4.5 15.0 - - + -
582B PHE 3.9 2.7 - - - -
583B GLU* 3.3 37.5 - - + -
683B ARG* 3.8 22.2 - - + -
684B TRP* 1.3 80.6 - - - +
686B LEU* 1.3 60.5 + - - +
687B GLN* 5.8 2.2 - - + +
696B ARG 3.6 1.0 - - - +
697B VAL* 3.2 7.6 - - - +
698B ARG* 3.0 47.0 + - - +
700B TYR* 3.8 30.7 - + - -
740B ARG* 5.6 1.6 - - - -
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B VAL* 4.7 3.4 - - + -
581B ASP* 3.4 5.9 - - - -
582B PHE* 2.7 60.6 + - + +
599B PHE* 3.9 15.7 - - + -
601B PHE* 3.3 67.5 - - + -
684B TRP* 4.1 0.4 - - - -
685B PHE* 1.3 75.5 - - - +
687B GLN* 1.3 76.3 + - - +
688B HIS* 4.3 7.9 - - + -
696B ARG 3.4 3.6 - - - +
697B VAL* 3.7 18.8 - - + +
722B LEU* 4.6 1.8 - - + -
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Residues in contact with GLN 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B ASP* 3.3 24.8 + - - +
685B PHE* 5.6 2.9 - - + +
686B LEU* 1.3 77.8 - - - +
688B HIS* 1.3 61.6 + - - +
689B ARG* 4.0 4.9 - - - +
694B TYR* 3.8 9.5 + - + +
695B ILE* 3.5 4.7 - - - -
696B ARG* 2.8 51.3 + - + +
698B ARG* 3.4 34.5 + - - +
746B PRO* 3.8 11.6 - - - +
1E NAG 3.5 31.7 + - - -
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Residues in contact with HIS 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ASN* 6.0 0.2 - - - -
579B GLY* 3.0 5.9 + - - -
580B VAL* 2.7 59.8 + - + +
601B PHE* 3.5 30.0 - + + -
602B GLY* 4.6 10.0 + - - -
610B TYR* 4.5 3.2 - + - -
686B LEU* 4.2 3.3 - - + -
687B GLN* 1.3 74.8 - - - +
689B ARG* 1.3 65.9 + - - +
690B PRO* 3.8 26.2 - - + +
693B GLY 5.4 0.4 - - - -
694B TYR 3.2 17.9 - - - -
695B ILE* 3.5 21.1 - - + +
714B ASP 5.5 3.6 + - - -
717B MET 3.9 19.1 + - - -
719B GLY* 4.2 9.9 - - - -
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Residues in contact with ARG 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B VAL 3.0 16.2 + - - -
581B ASP* 2.7 32.5 + - - -
687B GLN* 4.0 2.8 - - - +
688B HIS* 1.3 87.1 + - - +
690B PRO* 1.4 62.1 - - - +
691B GLN* 3.2 15.8 + - - +
692B VAL 3.3 2.4 + - - -
693B GLY 2.9 6.2 + - - -
694B TYR* 2.8 46.6 + - + -
742B ASN* 3.0 49.4 + - - +
743B ASP 3.5 16.2 - - - -
744B THR 3.0 15.5 + - - -
745B ILE* 4.1 10.1 - - + -
746B PRO* 3.7 21.7 - - + +
1E NAG 3.5 13.7 + - - -
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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