Contacts of the strand formed by residues 697 - 704 (chain B) in PDB entry 2FJU
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 THR 697 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B LEU* 3.7 25.1 - - + +
691B SER* 5.1 0.2 - - - -
695B VAL* 3.7 13.6 + - + +
696B ARG* 1.3 79.9 - - - +
698B TYR* 1.3 66.2 - - - +
718B LEU* 3.5 2.3 - - - -
719B SER* 2.7 41.4 + - - -
723B ASN 5.3 0.5 + - - -
724B SER* 4.9 4.5 - - - -
727B PRO* 4.3 3.1 - - - +
729B TRP* 3.5 18.7 - - - -
751B VAL* 4.7 1.8 - - - -
752B MET 3.3 8.3 - - - +
753B GLU* 4.0 4.0 - - + +
754B GLU 4.2 0.4 - - - +
759B LEU* 3.7 28.5 - - + -
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Residues in contact with TYR 698 (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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697B THR* 1.3 76.8 - - - +
699B VAL* 1.3 67.5 + - - +
700B GLU* 3.8 5.9 + - + -
715B ARG* 3.4 46.8 + - + -
716B THR* 3.6 24.0 - - + +
717B LYS 4.1 2.0 - - - +
718B LEU* 3.9 21.8 - - + -
729B TRP* 4.2 1.3 - - - -
751B VAL* 3.6 4.0 - - - +
752B MET* 2.8 63.7 + - + +
753B GLU 3.7 20.2 - - - -
754B GLU* 4.4 3.4 - - - -
755B GLY 4.7 0.4 - - - -
756B ASN* 2.6 37.1 + - - +
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Residues in contact with VAL 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B VAL* 3.9 23.3 - - + -
698B TYR* 1.3 82.3 - - - +
700B GLU* 1.3 68.8 + - - +
701B VAL* 4.2 8.3 - - + -
714B TYR 4.6 0.3 - - - -
715B ARG* 3.4 1.4 - - - +
716B THR* 2.7 45.6 + - + +
729B TRP* 4.1 20.2 - - + -
734B PHE* 4.9 1.7 - - - -
749B VAL* 3.8 27.6 - - + -
750B ALA 3.3 11.4 - - - +
751B VAL* 4.1 14.8 - - + -
791B LEU* 3.9 9.2 - - + -
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Residues in contact with GLU 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B TYR* 3.8 8.0 + - + -
699B VAL* 1.3 71.6 - - - +
701B VAL* 1.3 68.0 + - - +
702B GLU* 5.0 0.3 - - - +
713B ARG* 5.7 4.0 + - - -
714B TYR 3.3 8.5 - - - +
715B ARG* 2.7 52.3 + - + -
748B ARG* 3.2 34.7 + - - +
749B VAL* 3.4 1.6 - - - -
750B ALA* 2.9 33.9 + - - +
752B MET* 3.9 12.6 - - + +
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Residues in contact with VAL 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B ILE* 3.9 13.0 - - + -
684B VAL* 4.1 15.0 - - + -
699B VAL* 4.2 6.1 - - + -
700B GLU* 1.3 81.5 - - - +
702B GLU* 1.3 65.3 + - - +
713B ARG* 3.8 0.5 - - - +
714B TYR* 2.9 36.2 + - - +
734B PHE* 3.7 29.8 - - + -
736B PHE* 3.7 22.7 - - + -
747B LEU* 3.8 15.7 - - + -
748B ARG 3.1 11.7 - - - +
749B VAL* 4.3 10.8 - - + -
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Residues in contact with GLU 702 (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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633B LEU* 4.5 5.8 - - - +
700B GLU* 5.0 0.3 - - - +
701B VAL* 1.3 77.3 - - - +
703B LEU* 1.3 63.8 + - - +
704B PHE* 3.7 26.4 - - + -
712B ARG 4.6 1.3 - - - +
713B ARG* 3.4 43.7 + - + +
736B PHE* 3.8 12.3 - - - -
747B LEU* 3.6 5.4 - - - +
748B ARG* 2.9 71.5 + - + +
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Residues in contact with LEU 703 (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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680B LEU* 6.3 0.2 - - + -
702B GLU* 1.3 80.2 - - - +
704B PHE* 1.3 73.5 + - - +
705B GLY 4.0 1.0 + - - -
709B ASP* 4.1 11.7 - - + -
710B PRO* 3.5 47.7 + - + +
711B LYS* 5.2 8.7 + - - +
712B ARG 4.9 1.6 + - - -
736B PHE* 3.7 19.6 - - + -
739B ILE* 3.9 16.6 - - + -
745B ALA* 4.1 7.4 - - + -
746B SER 3.3 16.6 - - - +
747B LEU* 4.2 7.6 - - + +
766B ILE* 3.5 31.4 - - + -
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Residues in contact with PHE 704 (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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612B MET* 3.4 31.6 - - + -
614B GLN* 3.7 12.3 - - + +
633B LEU* 4.1 6.7 - - + -
637B GLN* 3.6 34.5 - - + +
702B GLU* 3.7 23.1 - - - -
703B LEU* 1.3 79.0 - - - +
705B GLY* 1.3 58.6 + - - +
744B LEU 4.1 0.7 - - - +
745B ALA* 3.1 6.1 - - - +
746B SER* 2.8 52.8 + - - +
748B ARG* 3.8 39.3 - - + -
763B ILE* 4.0 16.2 - - + -
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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