Contacts of the helix formed by residues 654 - 669 (chain A) in PDB entry 4XUF
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 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A PHE* 3.2 45.7 - - + +
646A LEU* 4.2 11.3 - - + +
652A SER 3.0 8.0 - - - +
653A SER* 1.3 79.9 - - - +
655A ARG* 1.3 62.9 + - - +
656A GLU 3.2 0.2 - - - -
657A ALA* 3.1 23.9 + - - +
658A LEU* 3.6 3.6 + - - +
832A LEU* 3.1 31.5 - - + +
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Residues in contact with ARG 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A LEU* 3.6 24.1 - - + +
648A GLU* 5.2 7.9 + - - -
652A SER* 3.1 30.8 + - - +
654A GLU* 1.3 78.4 - - - +
656A GLU* 1.3 64.2 + - + +
658A LEU* 3.1 15.2 + - - +
659A MET* 3.2 17.5 + - + +
685A GLY 5.0 2.4 + - - -
686A PRO* 4.4 19.7 - - - +
687A ILE* 3.5 33.2 - - + +
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Residues in contact with GLU 656 (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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652A SER 5.1 3.1 - - - +
653A SER* 3.6 18.5 + - - +
654A GLU 3.2 0.6 - - - -
655A ARG* 1.3 77.6 - - + +
657A ALA* 1.3 62.0 + - - +
659A MET* 3.2 21.4 + - + +
660A SER* 3.2 15.6 + - - -
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Residues in contact with ALA 657 (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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653A SER 4.3 1.7 + - - +
654A GLU* 3.1 19.1 + - + +
656A GLU* 1.3 78.9 - - - +
658A LEU* 1.3 59.3 + - - +
660A SER* 2.9 20.7 + - - -
661A GLU* 3.5 9.7 + - - +
832A LEU* 4.4 19.0 - - + +
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Residues in contact with LEU 658 (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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644A LYS* 3.7 44.9 - - + +
645A MET* 4.5 1.8 - - - -
646A LEU* 3.7 39.0 - - + -
654A GLU 3.6 1.2 + - - +
655A ARG 3.1 10.1 + - - +
657A ALA* 1.3 78.0 - - - +
659A MET* 1.3 64.6 + - - +
661A GLU* 3.2 18.9 + - - +
662A LEU* 3.2 12.8 + - - +
687A ILE* 4.0 30.1 - - + +
689A LEU* 3.8 23.6 - - + -
832A LEU* 4.9 5.1 - - + +
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Residues in contact with MET 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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655A ARG* 3.2 14.8 + - + +
656A GLU* 3.2 16.3 + - + +
658A LEU* 1.3 77.8 - - - +
660A SER* 1.3 62.1 + - - +
662A LEU* 3.1 13.4 + - + +
663A LYS* 3.1 21.5 + - + +
682A THR* 5.8 8.3 - - + -
687A ILE* 3.9 37.0 - - + -
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Residues in contact with SER 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 GLU 3.2 9.0 + - - -
657A ALA* 2.9 21.0 + - - -
659A MET* 1.3 79.3 - - - +
661A GLU* 1.3 56.7 + - - +
663A LYS* 3.3 13.6 + - - +
664A MET* 3.0 28.2 + - - +
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Residues in contact with GLU 661 (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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644A LYS* 3.1 28.4 + - - +
657A ALA 3.5 8.0 + - - +
658A LEU* 3.2 21.8 + - + +
659A MET 3.2 0.6 - - - -
660A SER* 1.3 80.7 + - - +
662A LEU* 1.3 60.2 + - - +
664A MET* 3.6 9.5 + - - +
665A MET* 3.3 25.0 + - + +
689A LEU* 4.6 7.6 - - + +
691A PHE* 5.2 0.2 - - - -
829A ASP* 4.1 1.5 - - - +
831A GLY* 4.2 5.7 - - - +
832A LEU* 4.7 5.7 - - - +
1001A P30 2.2 53.5 + - - +
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Residues in contact with LEU 662 (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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600A ASP* 3.5 30.5 - - + +
603A TRP* 5.6 0.2 - - + -
658A LEU 3.2 9.2 + - - +
659A MET* 3.1 13.8 + - + +
661A GLU* 1.3 75.1 - - - +
663A LYS* 1.3 63.9 + - - +
664A MET 3.1 1.8 - - - -
665A MET* 3.2 15.8 + - - +
666A THR* 3.4 19.6 + - + +
677A LEU* 4.6 6.7 - - + -
680A ALA* 3.6 28.0 - - + -
682A THR* 3.8 21.5 - - + -
687A ILE* 4.3 5.2 - - + -
689A LEU* 3.7 32.3 - - + +
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Residues in contact with LYS 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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600A ASP* 5.5 10.3 - - + +
659A MET* 3.1 12.9 + - + +
660A SER* 3.3 14.6 + - - +
662A LEU* 1.3 79.7 - - - +
664A MET* 1.3 59.8 + - - +
666A THR* 3.3 18.2 + - - +
667A GLN* 3.4 18.7 + - - +
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Residues in contact with MET 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 SER 3.0 15.6 + - - +
661A GLU* 3.6 9.6 - - - +
662A LEU 3.1 0.2 - - - -
663A LYS* 1.3 76.5 - - - +
665A MET* 1.3 66.3 + - + +
667A GLN* 3.2 16.8 - - + +
668A LEU* 3.0 47.3 + - + +
807A CYS* 4.5 19.3 - - + -
808A VAL 6.1 1.3 - - - +
1001A P30 3.6 43.7 - - + +
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Residues in contact with MET 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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603A TRP* 5.4 1.9 - - - -
661A GLU* 3.3 13.7 - - + +
662A LEU* 3.2 6.2 + - - +
664A MET* 1.3 81.0 - - - +
666A THR* 1.3 61.7 + - - +
667A GLN 3.3 0.7 + - - -
668A LEU* 3.4 15.6 + - - +
669A GLY* 3.5 13.7 + - - +
674A ILE* 5.5 1.6 - - - -
675A VAL* 4.4 12.1 - - + +
677A LEU* 3.6 28.7 - - + +
691A PHE* 3.7 38.1 - - + -
1001A P30 3.2 62.8 - - + +
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Residues in contact with THR 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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600A ASP* 3.8 19.1 + - - -
603A TRP* 3.4 54.1 + - + +
662A LEU* 3.5 24.1 + - + +
663A LYS* 3.3 13.3 + - - +
665A MET* 1.3 76.9 - - - +
667A GLN* 1.3 61.3 + - - +
669A GLY* 4.2 5.7 + - - -
677A LEU* 3.7 16.4 - - + -
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Residues in contact with GLN 667 (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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663A LYS* 3.4 20.1 + - - +
664A MET* 3.2 23.4 - - - +
666A THR* 1.3 77.9 + - - +
668A LEU* 1.3 67.0 + - - +
669A GLY* 3.2 3.5 + - - -
805A LYS* 4.2 11.6 + - - +
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Residues in contact with LEU 668 (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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664A MET* 3.0 48.5 + - + +
665A MET* 3.4 10.0 + - - +
667A GLN* 1.3 79.7 - - + +
669A GLY* 1.3 71.8 + - - +
674A ILE* 4.5 20.4 - - + -
801A PHE* 3.2 49.3 - - + -
802A LEU* 4.4 15.7 - - + -
805A LYS* 3.5 19.6 - - + +
807A CYS* 4.3 15.7 - - - -
1001A P30 4.6 7.6 - - + -
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Residues in contact with GLY 669 (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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603A TRP* 6.3 3.1 - - - -
665A MET 3.5 11.2 + - - +
666A THR 4.2 4.4 + - - -
667A GLN 3.2 4.9 - - - -
668A LEU* 1.3 98.9 - - - +
670A SER* 1.3 63.2 + - - -
671A HIS 3.8 0.7 + - - -
674A ILE* 5.7 0.9 - - - +
801A PHE* 4.6 3.4 - - - -
805A LYS* 5.6 0.9 - - - -
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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