Contacts of the strand formed by residues 612 - 621 (chain D) in PDB entry 1FVU
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 HIS 612 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608D SER* 3.3 6.9 - - - -
609D TYR 2.9 27.2 + - - +
610D GLU 3.6 9.7 + - - -
611D GLY* 1.3 82.3 - - - +
613D CYS* 1.3 64.5 + - - +
614D TYR* 3.4 27.3 + - + +
643D GLN* 4.8 14.5 + - - -
647D GLU* 5.4 0.7 - - - -
722D GLU* 3.2 24.6 + - + +
723D PHE* 3.5 13.0 - - - +
724D GLN* 3.0 40.8 - - + +
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Residues in contact with CYS 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D CYS* 2.0 48.5 - - + -
606D TRP* 4.4 4.7 - - + -
607D SER 3.2 7.0 - - - +
608D SER* 2.7 29.2 - - - -
611D GLY 5.6 0.4 - - - -
612D HIS* 1.3 77.4 - - - +
614D TYR* 1.3 64.0 + - - +
722D GLU* 3.2 7.4 - - - +
723D PHE* 3.0 46.7 + - + -
725D ALA* 4.6 4.3 - - - -
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Residues in contact with TYR 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D TRP* 3.5 2.6 - - - -
607D SER* 2.7 40.3 + - - +
609D TYR* 3.7 29.2 + + + -
612D HIS* 3.4 34.3 + - + +
613D CYS* 1.3 76.7 - - - +
615D ARG* 1.3 62.9 + - - +
640D VAL* 3.9 8.1 - - + -
647D GLU* 2.7 39.1 + - + +
650D PHE* 3.7 15.5 - + - -
651D VAL* 3.8 20.2 - - + -
654D LEU* 3.9 18.4 - - + +
720D VAL* 4.2 5.6 - - + -
721D CYS 3.3 7.6 - - - +
722D GLU* 3.3 28.9 - - + -
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Residues in contact with ARG 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D PRO 5.0 0.2 + - - -
605D ASP* 3.4 50.7 + - - +
606D TRP* 3.6 40.7 - - + +
614D TYR* 1.3 77.5 - - - +
616D PHE* 1.3 71.7 + - - +
617D PHE* 3.2 46.2 - - + -
633D GLN* 5.3 2.6 - - - +
654D LEU* 4.9 2.7 - - - -
720D VAL* 3.4 4.4 - - - +
721D CYS 3.0 30.5 + - - -
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Residues in contact with PHE 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D ARG* 1.3 88.5 + - - +
617D PHE* 1.3 70.1 + - - +
618D LYS* 4.3 4.9 - - + -
654D LEU* 3.3 34.2 - - + +
655D THR* 3.8 30.5 - - + -
657D GLU* 3.0 40.4 - - + -
658D MET* 3.6 21.3 - - + -
664D VAL* 4.3 6.7 - - + -
718D ASN* 3.7 28.3 - - + -
719D PHE 3.6 9.4 - - - -
720D VAL* 4.0 11.3 - - + +
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Residues in contact with PHE 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D TRP* 4.0 13.7 - + - -
615D ARG* 3.2 76.3 - - + -
616D PHE* 1.3 79.0 - - - +
618D LYS* 1.3 58.4 + - - +
619D GLU* 3.2 27.6 + - - +
629D PHE* 3.4 26.7 - + - -
633D GLN* 3.9 8.5 - - + -
718D ASN* 3.4 21.1 - - - +
719D PHE* 2.8 31.6 + + + +
721D CYS* 3.8 25.8 - - + -
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Residues in contact with LYS 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D PHE* 4.3 3.5 - - + -
617D PHE* 1.3 70.7 - - - +
619D GLU* 1.3 71.1 + - - +
620D TRP* 3.2 43.1 - - - +
657D GLU* 3.5 44.9 - - + +
658D MET* 4.6 3.6 - - - +
659D LEU* 4.4 9.5 - - - +
718D ASN* 3.4 14.1 - - - +
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Residues in contact with GLU 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D PHE* 3.2 34.4 - - - +
618D LYS* 1.3 87.4 + - - +
620D TRP* 1.3 60.0 + - - +
621D MET* 3.9 13.0 - - + -
629D PHE* 4.0 17.2 - - + -
717D LYS 3.3 10.9 - - - +
718D ASN* 2.9 17.0 - - - +
719D PHE* 3.7 19.5 - - + -
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Residues in contact with TRP 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B LEU* 4.3 22.4 - - + -
618D LYS* 3.2 43.5 + - - +
619D GLU* 1.3 72.4 - - - +
621D MET* 1.3 63.3 + - - +
659D LEU* 3.4 39.7 - - + -
662D ASP* 3.4 15.0 - - - -
716D PHE* 3.4 50.8 - - + -
717D LYS* 3.7 12.3 - - + +
718D ASN* 3.6 13.2 + - - -
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Residues in contact with MET 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D GLU* 4.2 13.2 - - + -
620D TRP* 1.3 80.2 - - - +
622D HIS* 1.3 66.1 + - - +
625D ASP* 3.7 35.9 - - + +
626D ALA* 4.0 2.7 - - - +
629D PHE* 3.9 25.4 - - + -
665D TRP* 2.9 23.0 + - - -
715D ARG 3.4 0.2 - - - +
716D PHE* 3.8 11.4 - - - -
717D LYS 3.0 17.6 + - - +
719D PHE* 3.9 27.4 - - + -
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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