Contacts of the helix formed by residues 668 - 683 (chain F) in PDB entry 5G04
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 668 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511F GLU 6.0 2.7 - - - -
635F TYR* 4.7 2.8 - - - -
662F LEU* 4.5 0.9 - - - +
665F ASN* 2.8 45.9 + - - +
666F PRO 3.4 2.8 + - - -
667F GLN* 1.3 73.8 - - - +
669F SER* 1.3 65.2 + - - +
670F VAL* 3.3 7.6 - - - -
671F LEU* 3.3 28.8 + - - +
672F LEU* 3.2 23.9 + - - +
498R ILE* 5.9 0.2 - - - -
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Residues in contact with SER 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513F SER* 5.3 6.4 + - - -
667F GLN 3.3 6.1 + - - -
668F SER* 1.3 70.5 - - - +
670F VAL* 1.3 66.0 + - - +
672F LEU* 3.3 12.5 + - - +
673F CYS* 2.9 30.7 + - - -
695F ALA* 4.1 7.6 - - - +
698F ILE* 5.5 1.6 - - - -
699F ASP* 3.4 22.4 + - - +
702F ASN* 3.4 34.9 + - - +
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Residues in contact with VAL 670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F SER* 4.8 6.7 - - - -
669F SER* 1.3 82.8 + - - +
671F LEU* 1.3 65.8 + - - +
673F CYS* 3.5 9.5 + - - +
674F HIS* 3.1 33.7 + - + -
704F LEU* 4.0 18.4 - - + -
496R GLN* 3.9 27.8 - - - +
497R GLY* 4.5 7.6 - - - -
498R ILE* 3.7 31.6 - - + +
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Residues in contact with LEU 671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635F TYR* 3.9 20.6 - - + -
639F TYR* 3.6 30.3 - - + -
658F PHE* 4.1 15.3 - - + +
661F ALA* 3.8 37.0 - - + +
662F LEU* 4.1 8.1 - - + +
665F ASN 4.1 5.8 - - - +
668F SER* 3.3 31.8 + - - +
670F VAL* 1.3 78.3 - - - +
672F LEU* 1.4 55.1 + - - +
674F HIS* 3.1 6.7 + - - +
675F ILE* 2.8 39.4 + - + +
498R ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662F LEU* 3.7 32.8 - - + -
667F GLN* 4.9 2.2 - - - +
668F SER 3.2 21.7 + - - +
669F SER* 3.3 7.2 + - - +
671F LEU* 1.4 77.8 - - - +
673F CYS* 1.3 51.3 + - - +
675F ILE* 3.2 8.2 + - + +
676F GLY* 2.8 32.9 + - - -
691F THR* 3.7 30.4 - - + +
692F LEU* 4.9 1.0 - - - +
694F LYS* 4.8 15.3 - - - +
695F ALA* 3.8 24.7 - - + +
698F ILE* 3.8 28.7 - - + -
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Residues in contact with CYS 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669F SER 2.9 28.6 + - - -
670F VAL* 3.6 9.6 - - - +
672F LEU* 1.3 75.2 - - - +
674F HIS* 1.3 57.1 + - - +
676F GLY* 3.2 1.0 + - - -
677F VAL* 2.9 36.9 + - - +
692F LEU* 3.9 14.6 - - + +
695F ALA* 4.5 4.2 - - - +
702F ASN* 5.7 0.9 - - - -
704F LEU* 4.3 8.7 - - + -
705F CYS* 3.5 39.9 - - - -
708F HIS* 4.0 19.3 - - + -
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Residues in contact with HIS 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639F TYR* 3.1 35.9 + + + -
643F MET* 5.3 9.2 - - + -
646F TYR* 5.5 7.8 - + - -
658F PHE* 4.0 27.0 - + + -
670F VAL* 3.1 29.5 + - + +
671F LEU* 3.1 11.3 + - - +
673F CYS* 1.3 77.6 - - + +
675F ILE* 1.3 65.9 + - - +
677F VAL* 3.3 8.7 + - - +
678F VAL* 3.2 26.3 + - - +
704F LEU* 4.7 10.6 - - + +
708F HIS* 5.9 1.8 - - - -
496R GLN 5.1 3.2 + - - -
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Residues in contact with ILE 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655F GLU* 4.2 14.6 - - + +
658F PHE* 3.4 30.3 - - + +
659F GLN* 4.2 11.0 - - - +
662F LEU* 3.7 46.4 - - + -
671F LEU* 2.8 24.0 + - + +
672F LEU* 3.5 9.9 - - + +
674F HIS* 1.3 72.0 - - - +
676F GLY* 1.3 65.1 + - - +
678F VAL* 3.0 17.2 + - - +
679F GLN* 3.0 38.3 + - + +
691F THR* 4.7 5.6 - - + -
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Residues in contact with GLY 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672F LEU 2.8 19.2 + - - -
673F CYS 3.2 4.6 + - - -
675F ILE* 1.3 71.8 - - - +
677F VAL* 1.3 62.3 + - - +
679F GLN* 3.0 17.5 + - - +
680F HIS* 2.9 22.2 + - - +
688F ALA* 3.6 10.8 - - - +
691F THR* 4.5 2.4 - - - +
692F LEU* 4.4 19.7 - - - -
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Residues in contact with VAL 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646F TYR* 4.1 23.9 - - + +
673F CYS 2.9 18.0 + - - +
674F HIS* 3.3 6.9 + - - +
676F GLY* 1.3 75.0 - - - +
678F VAL* 1.3 56.2 + - - +
680F HIS* 3.6 15.0 + - + +
681F ALA* 3.2 26.4 + - + +
692F LEU* 5.3 0.7 - - + -
708F HIS* 3.5 46.4 - - + +
712F VAL* 5.6 4.5 - - + -
780F ASP* 5.6 6.7 - - + +
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Residues in contact with VAL 678 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646F TYR* 3.7 23.3 - - + -
651F PHE* 3.2 37.2 - - + +
654F ALA* 4.0 4.5 - - + -
655F GLU* 3.6 20.9 - - + +
658F PHE* 3.7 23.8 - - + -
674F HIS 3.2 15.7 - - - +
675F ILE 3.0 8.3 + - - +
677F VAL* 1.3 75.0 - - - +
679F GLN* 1.3 64.6 + - - +
681F ALA* 3.1 8.1 + - - +
682F LEU* 3.0 22.8 + - + +
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Residues in contact with GLN 679 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655F GLU* 3.3 32.5 + - + +
659F GLN* 5.2 4.0 - - - +
675F ILE* 3.0 26.1 + - - +
676F GLY* 3.5 7.2 - - - +
678F VAL* 1.3 73.9 - - - +
680F HIS* 1.3 64.1 + - - +
682F LEU* 3.2 11.9 + - - +
683F LYS 3.2 4.0 + - - -
684F LYS* 3.1 39.5 + - + +
687F LYS* 3.7 12.4 + - + +
688F ALA* 3.4 23.4 - - + -
691F THR* 3.0 30.1 + - - -
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Residues in contact with HIS 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676F GLY 2.9 12.9 + - - +
677F VAL* 3.7 18.0 + - - +
679F GLN* 1.3 77.4 - - - +
681F ALA* 1.3 60.1 + - - +
683F LYS* 3.0 21.8 + - - +
685F SER* 4.2 14.6 - - - +
688F ALA* 3.6 9.1 - - + +
711F SER* 4.6 6.5 + - - -
712F VAL* 3.9 41.9 - - + -
715F ALA* 3.6 26.1 - - + +
780F ASP 3.6 24.3 + - - -
781F LYS* 3.9 15.4 + - - -
782F ARG 6.0 0.4 - - - -
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Residues in contact with ALA 681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646F TYR* 5.2 2.2 - - + -
651F PHE* 4.0 37.5 - - + -
677F VAL 3.2 14.0 + - - +
678F VAL* 3.1 10.6 + - - +
680F HIS* 1.3 82.9 + - - +
682F LEU* 1.3 59.6 + - - +
683F LYS* 3.3 15.9 + - - +
780F ASP 5.5 4.3 - - - +
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Residues in contact with LEU 682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651F PHE* 3.5 13.5 - - + -
652F SER* 3.5 35.2 - - - +
655F GLU* 3.5 35.2 - - + +
678F VAL 3.0 17.9 + - - +
679F GLN* 3.2 10.7 + - - +
681F ALA* 1.3 73.9 - - - +
683F LYS* 1.3 71.8 + - - +
684F LYS* 3.3 19.6 + - + +
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Residues in contact with LYS 683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F GLN 3.2 0.2 + - - -
680F HIS 3.0 17.0 + - - +
681F ALA 4.0 14.6 - - - +
682F LEU* 1.3 79.9 - - - +
684F LYS* 1.3 55.3 + - - +
685F SER* 2.9 20.5 + - - +
686F GLU* 4.6 3.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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