Contacts of the helix formed by residues 652 - 667 (chain A) in PDB entry 4FUL
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 GLU 652 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL 5.4 0.4 - - - +
203A THR* 3.5 8.9 + - - -
204A SER* 2.9 46.9 + - - -
205A LYS* 3.3 19.5 + - - -
650A SER 3.5 4.3 + - - +
651A LEU* 1.3 74.0 - - - +
653A ASP* 1.3 57.1 + - - +
654A ASP* 3.8 11.3 - - + +
655A ASP* 2.8 38.4 + - - +
656A VAL* 3.0 10.7 + - - +
684A ARG* 3.6 2.2 - - - +
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO 5.7 0.2 - - - +
201A TRP* 6.3 1.6 - - + -
202A VAL 5.6 2.7 - - - +
652A GLU* 1.3 71.2 - - - +
654A ASP* 1.3 61.5 + - - +
656A VAL* 3.3 2.6 + - - +
657A LEU* 3.0 33.3 + - + +
684A ARG* 2.9 25.7 + - - +
687A ARG* 5.1 8.8 - - - +
688A ASN* 2.9 36.2 + - - +
691A ILE* 3.7 20.2 - - + +
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Residues in contact with ASP 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 4.2 14.8 + - - +
202A VAL 3.6 19.4 + - - +
203A THR* 3.2 20.3 + - - -
205A LYS* 2.7 30.2 + - - +
291A GLN* 4.0 13.3 - - - +
652A GLU* 3.2 14.3 - - + +
653A ASP* 1.3 75.3 - - - +
655A ASP* 1.4 60.5 + - - +
657A LEU* 3.5 19.9 + - - +
658A HIS* 3.3 29.1 + - - -
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Residues in contact with ASP 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 2.9 35.4 + - - -
651A LEU* 3.4 30.1 - - + +
652A GLU* 2.8 24.0 + - - +
654A ASP* 1.4 70.4 - - - +
656A VAL* 1.4 63.2 + - - +
657A LEU 3.2 1.8 - - - -
658A HIS* 3.1 21.3 + - - +
659A TYR* 3.2 30.7 - - + -
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A LEU* 3.9 18.1 - - + +
652A GLU 3.0 9.6 + - - +
653A ASP 3.7 6.5 - - - +
655A ASP* 1.4 73.0 - - - +
657A LEU* 1.3 54.2 + - - +
659A TYR 3.2 1.6 + - - +
660A LEU* 2.6 44.9 + - + +
663A LEU* 4.7 5.7 - - + +
680A PHE* 4.3 14.6 - - + -
681A LEU* 5.9 0.4 - - + -
684A ARG* 3.5 48.9 - - + +
691A ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 4.0 22.2 - - + +
653A ASP* 3.0 23.2 + - + +
654A ASP 3.6 8.5 - - - +
655A ASP 3.2 0.4 - - - -
656A VAL* 1.3 73.0 - - - +
658A HIS* 1.3 64.0 + - + +
659A TYR 3.5 0.3 + - - -
660A LEU* 3.8 14.4 + - + +
661A LEU 5.1 0.5 + - - -
688A ASN* 5.2 1.6 - - - +
690A ARG* 3.7 43.5 - - + +
691A ILE* 3.7 27.8 - - + -
694A PHE* 4.2 17.3 - - + -
698A PHE* 5.7 1.6 - - - -
846A GLN* 3.9 10.8 + - - +
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Residues in contact with HIS 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 5.6 3.4 - - + -
654A ASP* 3.3 36.7 + - - -
655A ASP* 3.1 21.2 + - - +
657A LEU* 1.3 76.0 - - - +
659A TYR* 1.3 72.8 + + + +
846A GLN* 3.1 27.8 + - - +
849A ARG* 3.9 27.1 + - + +
850A ILE* 3.3 21.3 - - + +
853A SER* 3.7 27.2 - - - -
856A GLU* 6.0 1.1 - - - -
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Residues in contact with TYR 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A VAL* 3.4 42.4 - - + +
628A MET* 3.5 24.7 - - + -
651A LEU* 5.0 4.5 - - + -
655A ASP* 3.2 34.9 + - + +
656A VAL 3.2 2.6 + - - -
658A HIS* 1.3 87.9 - + + +
660A LEU* 1.4 63.1 + - - +
661A LEU 3.3 2.5 - - - -
662A GLN* 3.1 8.7 + - + +
663A LEU* 2.9 40.3 + - + +
850A ILE* 3.6 37.7 - - + +
853A SER* 4.9 5.0 + - - -
854A ILE* 6.1 0.2 - - - +
1026A LEU* 3.8 25.5 - - + +
1030A LEU* 4.3 2.2 - - + -
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A VAL* 2.6 28.5 + - + +
657A LEU* 3.8 13.9 + - + +
658A HIS 3.7 1.8 - - - -
659A TYR* 1.4 68.8 - - - +
661A LEU* 1.4 53.2 + - - +
663A LEU* 3.1 7.3 + - + +
664A VAL* 2.8 43.5 + - + +
681A LEU* 3.7 28.0 - - + +
684A ARG* 6.1 0.2 - - + -
691A ILE* 3.5 47.3 - - + +
694A PHE* 3.7 15.3 - - + -
695A LEU* 3.6 19.5 - - + +
698A PHE* 4.0 10.8 - - + -
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU 5.1 1.0 + - - -
659A TYR 3.3 1.2 - - - -
660A LEU* 1.4 75.4 - - - +
662A GLN* 1.4 57.6 + - - +
664A VAL* 3.3 4.8 + - - +
665A GLN* 3.0 46.7 + - + +
698A PHE* 3.7 50.4 - - + +
842A MET* 3.5 50.9 - - + +
843A LEU* 3.8 22.0 - - + +
846A GLN* 4.1 22.1 - - + +
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Residues in contact with GLN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A MET* 3.9 17.5 - - + -
658A HIS 5.5 0.7 - - - +
659A TYR* 3.1 9.6 + - - +
661A LEU* 1.4 74.9 - - + +
663A LEU* 1.4 54.4 + - - +
665A GLN* 3.3 8.7 + - - +
666A ALA* 2.8 33.8 + - - +
843A LEU* 3.5 43.4 + - - +
846A GLN* 4.5 10.6 - - + +
847A ILE* 4.1 9.7 - - - +
850A ILE* 4.9 8.9 - - + +
1030A LEU* 3.3 47.2 - - + +
1033A MET* 4.2 14.3 - - + +
1034A MET* 4.2 4.2 + - - +
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A MET* 3.7 25.4 - - + -
631A LEU* 4.4 4.5 - - + -
648A LEU* 3.7 31.4 - - + -
651A LEU* 4.9 6.3 - - + -
656A VAL* 4.7 7.0 - - + +
659A TYR* 2.9 35.5 + - + +
660A LEU* 3.5 10.3 - - - +
662A GLN* 1.4 73.5 - - - +
664A VAL* 1.4 63.0 + - - +
666A ALA* 3.4 10.4 + - + -
667A VAL* 3.7 7.3 + - - +
677A LEU* 3.7 14.4 - - + +
680A PHE* 4.4 19.7 - - + -
681A LEU* 3.5 26.5 - - + +
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A LEU* 2.8 27.9 + - + +
661A LEU* 3.7 5.4 - - + +
663A LEU* 1.4 70.8 - - - +
665A GLN* 1.3 70.1 + - - +
667A VAL* 3.2 9.2 - - - +
681A LEU* 3.8 15.3 - - + -
695A LEU* 3.6 28.9 - - + -
698A PHE* 4.1 33.7 - - + +
699A LEU* 3.9 22.9 - - + -
702A GLU* 5.3 0.9 - - + -
713A PHE* 3.2 30.0 - - + -
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Residues in contact with GLN 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A LEU* 3.0 34.9 + - + +
662A GLN* 3.5 9.0 - - - +
663A LEU 3.3 0.2 - - - -
664A VAL* 1.3 80.0 - - - +
666A ALA* 1.4 57.0 + - - +
668A LYS* 2.8 66.0 + - - +
698A PHE 5.4 1.0 + - - -
702A GLU* 2.7 29.6 + - - +
713A PHE* 4.8 0.7 - - - -
839A ARG* 6.0 0.6 - - - +
842A MET* 6.4 0.4 - - - +
843A LEU* 4.3 18.4 - - + +
1033A MET* 6.4 1.1 - - + -
1037A THR* 3.3 35.2 - - + +
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A MET* 5.9 0.9 - - - -
631A LEU* 3.8 21.3 - - + +
641A ARG* 3.4 17.0 + - - -
662A GLN 2.8 20.3 + - - +
663A LEU* 3.8 7.2 - - + +
664A VAL 3.4 0.6 - - - -
665A GLN* 1.4 69.8 - - - +
667A VAL* 1.3 55.2 + - - +
668A LYS 3.2 0.7 - - - -
669A PHE* 3.0 29.9 + - - +
677A LEU* 3.7 19.1 - - + -
1033A MET* 4.2 13.9 - - + -
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Residues in contact with VAL 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LEU 3.7 3.3 + - - +
664A VAL 3.2 14.6 - - - +
665A GLN 2.9 0.4 + - - -
666A ALA* 1.3 76.8 - - - +
668A LYS* 1.4 51.8 + - - +
669A PHE 3.2 0.2 - - - -
670A GLU* 3.2 13.2 + - + +
673A HIS 5.8 0.7 - - - +
675A SER* 5.6 0.4 - - - +
677A LEU* 3.8 13.9 - - + -
678A ALA* 4.6 12.6 - - + +
681A LEU* 3.5 31.6 - - + -
712A ARG* 2.8 50.5 + - - +
713A PHE* 3.5 21.5 - - + -
716A ILE* 3.9 13.2 - - + -
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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