Contacts of the strand formed by residues 717 - 724 (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 LYS 717 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 6.0 3.8 - - - +
492B LEU* 6.2 2.6 - - - +
619D GLU 3.3 4.9 - - - +
620D TRP* 4.0 6.7 - - + -
621D MET 3.0 27.7 + - - +
662D ASP* 2.6 31.8 + - - +
663D VAL* 3.4 36.2 - - + +
665D TRP* 3.6 32.8 - - + +
700D ALA* 5.1 0.2 - - + -
711D ILE* 3.9 13.9 - - + -
715D ARG* 3.6 17.4 + - + +
716D PHE* 1.3 81.6 + - - +
718D ASN* 1.3 72.3 + - - +
719D PHE* 3.7 5.4 - - - -
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Residues in contact with ASN 718 (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* 3.7 18.0 - - + -
617D PHE 3.4 11.9 - - - +
618D LYS* 3.4 33.4 - - - +
619D GLU 2.9 21.9 - - - +
620D TRP* 3.6 24.8 - - - -
658D MET* 3.7 28.4 - - - +
659D LEU* 4.5 0.2 - - - +
662D ASP* 5.1 0.8 + - - -
663D VAL 4.3 4.7 + - - +
664D VAL* 3.4 7.1 - - + +
665D TRP* 3.1 19.8 + - - -
717D LYS* 1.3 79.9 - - - +
719D PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 719 (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* 3.6 3.6 - - - -
617D PHE* 2.8 47.2 + - + -
619D GLU* 3.7 21.1 - - + -
621D MET* 3.9 28.3 - - + -
626D ALA* 3.7 18.8 - - + -
629D PHE* 3.4 35.7 - + - -
630D CYS* 3.9 7.2 - - - -
639D LEU* 3.6 17.3 - - + -
664D VAL* 3.2 9.8 - - - +
665D TRP* 3.9 8.7 - - + -
717D LYS 3.7 7.2 - - - -
718D ASN* 1.3 82.7 - - - +
720D VAL* 1.3 64.7 + - - +
721D CYS* 3.8 18.2 - - - -
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Residues in contact with VAL 720 (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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614D TYR* 4.2 7.0 - - + -
615D ARG 3.4 17.5 - - - +
616D PHE* 4.0 17.7 - - + +
630D CYS* 4.4 0.4 - - - -
639D LEU* 3.5 8.3 - - - +
640D VAL* 2.8 45.3 + - + +
651D VAL* 3.9 28.3 - - + +
654D LEU* 5.2 2.0 - - + -
655D THR* 4.9 2.7 - - + -
664D VAL* 3.7 20.4 - - + +
665D TRP 3.9 2.0 + - - -
719D PHE* 1.3 81.0 - - - +
721D CYS* 1.3 73.4 + - - +
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Residues in contact with CYS 721 (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* 3.6 24.9 - - + -
614D TYR* 3.3 5.0 - - - -
615D ARG 3.0 29.0 + - - -
617D PHE* 3.8 20.9 - - + -
629D PHE* 4.4 2.7 - - - -
630D CYS* 2.0 52.0 - - + +
633D GLN* 4.9 0.4 - - - -
637D ALA* 5.2 0.4 - - + -
638D HIS 3.2 5.8 - - - +
719D PHE* 3.8 12.8 - - - -
720D VAL* 1.3 76.9 - - - +
722D GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 722 (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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286C ASP* 4.4 5.9 - - - +
606D TRP* 4.4 0.7 - - - -
612D HIS* 3.2 23.0 - - + -
613D CYS 3.2 9.4 - - - +
614D TYR* 3.3 32.8 - - + -
636D GLY 4.3 0.5 - - - +
637D ALA* 3.2 1.6 - - - -
638D HIS* 2.7 34.6 + - - +
639D LEU 4.7 1.3 - - - +
640D VAL* 3.3 12.2 - - - +
641D SER* 2.8 30.9 + - - -
647D GLU* 3.6 0.5 - - - +
721D CYS* 1.3 77.7 - - - +
723D PHE* 1.3 70.9 + - - +
1002D MG 2.5 23.9 - - - -
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Residues in contact with PHE 723 (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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601D ASP 5.4 1.6 - - - -
602D CYS* 3.1 40.2 - - + -
603D PRO* 4.3 0.4 - - + -
606D TRP* 3.4 33.9 - + - -
612D HIS* 3.5 10.7 - - - +
613D CYS* 3.0 37.5 + - + -
634D GLN* 3.1 37.9 - - + -
635D THR 4.7 6.7 - - - +
636D GLY 4.3 5.8 - - - +
637D ALA* 3.8 21.1 - - + +
722D GLU* 1.3 80.3 - - - +
724D GLN* 1.3 76.5 + - - +
725D ALA* 4.6 2.7 - - + -
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Residues in contact with GLN 724 (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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611D GLY 4.4 1.8 - - - +
612D HIS* 3.0 39.1 + - + +
636D GLY 5.5 0.6 + - - -
723D PHE* 1.3 87.2 - - - +
725D ALA* 1.3 63.8 + - - +
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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