Contacts of the helix formed by residues 670 - 688 (chain A) in PDB entry 1CEZ
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 PRO 670 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 4.1 10.4 - - + +
655A ILE* 3.3 42.4 - - + +
656A GLN* 6.3 0.4 - - - +
659A ILE* 4.0 15.7 - - + -
667A PHE* 3.4 19.2 - - + +
668A THR 3.2 14.8 - - - +
669A GLN* 1.3 86.2 - - - +
671A ASN* 1.3 62.1 + - + +
673A ALA* 3.6 1.3 + - + -
674A ALA* 3.3 5.9 + - - +
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Residues in contact with ASN 671 (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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647A ARG* 3.7 32.6 + - - +
651A LEU* 3.7 22.9 - - + +
669A GLN* 2.9 2.1 + - + -
670A PRO* 1.3 78.3 - - + +
672A GLN* 1.3 66.0 + - + +
674A ALA* 3.3 3.6 + - - +
675A GLY* 2.9 22.0 + - - -
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Residues in contact with GLN 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A GLU* 6.2 0.2 - - - +
609A VAL* 3.5 33.4 + - - +
610A LYS* 2.9 35.3 - - - +
611A LEU* 3.4 5.4 - - - +
616A LEU* 4.3 13.1 - - + +
647A ARG* 5.8 1.6 - - - +
669A GLN* 3.0 25.6 + - + +
671A ASN* 1.3 77.6 - - + +
673A ALA* 1.3 60.6 + - - +
675A GLY* 3.8 1.9 - - - +
676A TYR* 2.9 30.7 + - - +
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Residues in contact with ALA 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 4.1 11.5 - - + +
619A GLN* 3.9 11.2 - - - +
620A TRP* 3.1 17.9 + - - +
655A ILE* 3.8 4.9 - - + -
667A PHE* 3.5 34.8 - - + -
669A GLN 3.1 10.1 + - - +
670A PRO* 3.8 10.1 - - + +
671A ASN 3.2 0.2 - - - -
672A GLN* 1.3 77.3 - - - +
674A ALA* 1.3 63.2 + - - +
676A TYR* 3.2 2.3 + - - +
677A MET* 3.0 18.5 + - - +
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Residues in contact with ALA 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A TRP* 4.7 0.4 - - - -
647A ARG* 3.6 18.2 - - + +
650A VAL* 4.3 9.1 - - - +
651A LEU* 3.5 39.5 - - + +
655A ILE* 3.4 15.2 - - + +
670A PRO 3.3 2.5 + - - +
671A ASN* 3.3 9.7 + - - +
673A ALA* 1.3 77.8 - - - +
675A GLY* 1.3 66.8 + - - +
677A MET* 3.3 2.1 + - - +
678A ALA* 3.1 18.4 + - - +
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Residues in contact with GLY 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ARG* 3.2 39.0 + - - +
671A ASN 2.9 12.0 + - - -
672A GLN* 3.8 3.1 - - - -
673A ALA 3.3 0.2 - - - -
674A ALA* 1.3 77.8 - - - +
676A TYR* 1.3 61.6 + - - +
677A MET 3.6 0.2 + - - -
678A ALA* 3.6 8.3 + - - +
679A LYS* 3.6 12.5 + - - +
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Residues in contact with TYR 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ILE 4.6 0.5 + - - -
582A LEU* 3.6 31.9 - - + +
585A ASP* 2.6 34.4 + - - +
613A THR* 3.7 25.6 - - + -
616A LEU* 3.5 33.0 - - + -
617A ALA* 3.8 8.0 - - - +
620A TRP* 3.7 16.4 - + - -
672A GLN 2.9 17.9 + - - +
673A ALA 3.5 2.0 - - - +
674A ALA 3.2 0.2 - - - -
675A GLY* 1.3 76.4 - - - +
677A MET* 1.3 61.4 + - + +
679A LYS* 3.6 10.7 + - + +
680A LEU* 3.4 42.8 + - + +
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Residues in contact with MET 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A VAL* 4.0 21.1 - - + -
582A LEU* 4.3 6.7 - - + -
620A TRP* 3.4 64.6 - - + -
625A VAL* 3.8 19.7 - - + -
629A VAL* 5.6 5.2 - - + -
630A THR* 6.4 0.4 - - - -
650A VAL* 4.4 9.0 - - + -
673A ALA 3.0 7.3 + - - +
674A ALA 3.3 3.5 + - - +
676A TYR* 1.3 75.4 - - - +
678A ALA* 1.3 67.1 + - - +
680A LEU* 3.1 7.9 + - + +
681A ILE* 2.9 50.8 + - + +
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Residues in contact with ALA 678 (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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646A PHE* 4.1 13.9 - - + +
647A ARG* 3.5 37.2 - - + +
650A VAL* 4.6 7.3 - - + +
674A ALA 3.1 6.5 + - - +
675A GLY 3.8 4.3 - - - +
677A MET* 1.3 76.4 - - - +
679A LYS* 1.3 58.1 + - - +
681A ILE* 3.8 5.7 - - - +
682A TRP* 2.9 32.9 + - - +
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Residues in contact with LYS 679 (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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675A GLY 3.6 8.8 + - - +
676A TYR* 3.6 12.9 + - + +
677A MET 3.2 0.4 - - - -
678A ALA* 1.3 80.1 - - - +
680A LEU* 1.3 59.9 - - + +
682A TRP* 4.2 6.7 - - + +
683A GLU* 2.8 48.7 + - + +
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A VAL* 3.7 25.8 - - + +
581A ILE* 3.7 38.4 - - + +
582A LEU* 3.8 24.2 - - + -
585A ASP* 4.9 0.9 - - - +
676A TYR* 3.4 38.7 + - + +
677A MET* 3.1 16.9 + - + +
679A LYS* 1.3 81.7 - - + +
681A ILE* 1.3 55.8 + - - +
683A GLU* 3.3 10.8 + - - +
684A SER* 2.7 40.6 + - - -
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Residues in contact with ILE 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 4.7 4.3 - - + -
578A VAL* 4.1 13.9 - - + -
629A VAL* 4.9 5.8 - - + +
630A THR* 4.9 8.5 - - + +
633A SER* 3.9 26.0 - - - +
634A VAL* 3.8 33.0 - - + +
650A VAL* 5.0 6.7 - - + -
677A MET* 2.9 48.1 + - + +
678A ALA* 3.8 5.6 - - - +
680A LEU* 1.3 76.4 - - - +
682A TRP* 1.3 58.5 + - - +
684A SER* 3.0 2.5 + - - -
685A VAL* 2.8 32.5 + - + +
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Residues in contact with TRP 682 (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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637A LEU* 6.6 0.2 - - + -
638A ALA* 5.4 12.3 - - + -
678A ALA 2.9 18.7 + - - +
679A LYS* 4.2 6.3 - - + +
681A ILE* 1.3 78.9 - - - +
683A GLU* 1.3 56.1 + - - +
685A VAL* 3.1 21.1 - - + +
686A SER* 2.7 53.0 + - - -
693A VAL* 3.9 34.5 - - + -
696A MET* 5.9 6.7 - - + -
697A ASN* 5.6 7.2 - - - -
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Residues in contact with GLU 683 (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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581A ILE* 3.4 29.8 - - + +
679A LYS* 2.8 42.2 + - + +
680A LEU* 3.6 10.3 - - - +
682A TRP* 1.3 82.0 - - + +
684A SER* 1.3 63.7 + - - +
686A SER* 3.6 11.0 + - - -
687A VAL* 3.6 21.7 - - + +
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Residues in contact with SER 684 (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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574A VAL* 3.5 24.5 - - - -
577A LYS* 3.8 10.3 + - - +
578A VAL* 3.1 27.2 + - - +
581A ILE* 4.2 7.2 - - - +
680A LEU 2.7 21.6 + - - -
681A ILE 3.0 5.4 + - - -
683A GLU* 1.3 75.4 - - - +
685A VAL* 1.3 60.6 + - - +
687A VAL* 3.3 11.5 + - - +
688A THR* 2.6 30.8 + - - -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 3.6 24.9 - - + -
634A VAL* 4.1 23.6 - - + -
681A ILE* 2.8 23.2 + - + +
682A TRP* 3.1 39.5 - - + +
684A SER* 1.3 72.6 - - - +
686A SER* 1.3 67.1 + - - +
688A THR* 3.9 7.4 - - - -
689A VAL* 2.9 38.8 + - + +
693A VAL* 5.2 2.5 - - + -
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Residues in contact with SER 686 (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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682A TRP* 2.7 51.9 + - - -
683A GLU* 3.8 9.0 - - - -
684A SER 3.2 0.4 - - - -
685A VAL* 1.3 78.9 - - - +
687A VAL* 1.3 61.0 + - - +
690A VAL* 3.3 26.1 - - - +
693A VAL* 4.2 13.6 - - - +
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Residues in contact with VAL 687 (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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554A VAL* 5.7 3.1 - - - +
577A LYS* 4.3 18.3 - - + +
683A GLU* 3.6 17.5 - - + +
684A SER* 3.3 15.5 + - - +
686A SER* 1.3 79.4 - - - +
688A THR* 1.3 63.4 + - - +
689A VAL 3.6 0.2 - - - -
690A VAL* 3.6 17.6 - - + +
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Residues in contact with THR 688 (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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554A VAL* 4.3 19.3 - - - +
555A GLY* 4.4 5.0 - - - -
558A ALA* 4.8 4.2 - - + +
570A ILE* 4.3 6.7 - - + -
573A ILE* 3.4 36.8 - - + -
574A VAL* 4.1 14.9 - - + +
577A LYS* 3.5 19.3 - - - +
684A SER 2.6 23.8 + - - -
685A VAL* 3.0 8.8 + - - -
687A VAL* 1.3 80.4 - - - +
689A VAL* 1.3 70.1 + - + +
690A VAL* 3.6 1.0 + - - -
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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
------------------------------------------------------------
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