Contacts of the helix formed by residues 662 - 684 (chain A) in PDB entry 1SL1
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 662 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A VAL* 4.7 7.0 - - - -
660A CYS* 3.2 8.4 - - - +
661A ARG* 1.3 112.6 - - + +
663A GLU* 1.3 64.0 + - - +
664A GLU* 3.3 10.9 + - - +
665A ILE* 3.1 27.9 + - + +
666A ALA* 3.1 17.3 + - - +
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Residues in contact with GLU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A VAL* 4.5 17.0 - - + +
662A THR* 1.3 72.5 - - - +
664A GLU* 1.3 63.5 + - - +
666A ALA* 3.0 5.5 + - - +
667A GLN* 2.9 37.5 + - - +
696A MET* 3.2 29.5 - - + +
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A THR* 3.2 9.1 + - - +
663A GLU* 1.3 80.1 - - - +
665A ILE* 1.3 62.4 + - + +
667A GLN* 3.3 16.2 + - - +
668A VAL* 3.1 32.9 + - + +
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Residues in contact with ILE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LEU* 4.5 14.8 - - + -
645A ASP* 3.6 49.6 - - + +
646A PHE* 4.5 2.5 - - + -
660A CYS* 3.6 14.4 - - + -
661A ARG* 3.8 29.2 - - + +
662A THR* 3.1 21.8 + - + +
664A GLU* 1.3 76.6 - - + +
666A ALA* 1.3 60.8 + - - +
668A VAL* 3.0 10.1 + - - +
669A VAL* 2.8 33.9 + - + +
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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
----------------------------------------------------------
470A VAL* 4.4 6.1 - - + -
471A GLN 4.8 0.2 - - - +
472A ALA* 4.1 8.2 - - + +
660A CYS* 3.6 25.5 - - + +
662A THR 3.1 11.1 + - - +
663A GLU* 3.0 9.9 + - - +
665A ILE* 1.3 77.0 - - - +
667A GLN* 1.3 62.5 + - - +
669A VAL* 3.3 1.6 + - - +
670A ILE* 3.0 28.4 + - - +
696A MET* 3.5 27.6 - - + -
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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
----------------------------------------------------------
663A GLU* 2.9 22.9 + - - +
664A GLU* 3.6 17.3 - - - +
666A ALA* 1.3 76.0 - - - +
668A VAL* 1.3 55.3 + - + +
670A ILE* 3.4 8.8 + - - +
671A GLU* 2.7 44.0 + - - +
696A MET* 3.1 25.8 - - + +
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Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A LEU* 4.5 0.4 - - + -
636A LYS* 4.0 22.0 - - + -
638A LEU* 4.1 19.5 - - + -
664A GLU* 3.1 23.7 + - + +
665A ILE* 3.0 11.8 + - + +
667A GLN* 1.3 78.3 - - + +
669A VAL* 1.3 54.7 + - - +
671A GLU* 3.4 13.5 + - + +
672A THR* 2.6 47.8 + - - +
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ALA* 4.2 7.9 - - + -
474A ILE* 4.1 20.2 - - + -
629A THR* 4.8 6.2 - - + +
633A LEU* 3.8 36.1 - - + -
638A LEU* 5.1 1.6 - - + -
646A PHE* 4.5 7.4 - - + -
656A ILE* 5.7 0.7 - - + -
658A VAL* 4.3 15.9 - - + -
660A CYS* 4.0 15.5 - - - -
665A ILE* 2.8 22.8 + - + +
666A ALA* 3.3 9.4 + - - +
668A VAL* 1.3 75.4 - - - +
670A ILE* 1.3 58.9 + - - +
672A THR* 3.7 0.9 - - - -
673A ALA* 2.9 29.3 + - + +
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Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ALA* 4.1 14.8 - - + -
474A ILE* 4.2 17.6 - - + +
666A ALA 3.0 21.0 + - - +
667A GLN* 3.6 6.7 - - + +
669A VAL* 1.3 77.5 - - - +
671A GLU* 1.3 64.3 + - + +
673A ALA* 3.4 3.3 + - - +
674A GLN* 3.3 18.9 + - - +
692A THR* 4.7 2.3 + - - -
694A GLY* 3.9 20.9 - - - +
695A LYS 3.9 31.9 - - - +
696A MET* 4.3 16.2 - - + +
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Residues in contact with GLU 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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636A LYS* 6.1 1.4 - - - -
667A GLN* 2.7 35.6 + - - +
668A VAL* 3.6 16.6 - - + +
670A ILE* 1.3 75.2 - - + +
672A THR* 1.3 63.9 + - - +
674A GLN* 3.3 9.3 + - - +
675A GLU* 3.0 35.9 + - - +
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Residues in contact with THR 672 (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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629A THR* 3.9 8.3 - - + +
632A MET* 3.6 32.3 - - + -
633A LEU* 3.6 27.5 - - + +
636A LYS* 3.4 27.2 - - - +
668A VAL* 2.6 25.5 + - - +
669A VAL 3.7 1.6 - - - -
671A GLU* 1.3 78.1 - - - +
673A ALA* 1.3 52.7 + - - +
675A GLU* 3.1 10.6 + - - +
676A ALA* 2.8 32.6 + - - +
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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
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474A ILE* 4.0 27.8 - - + -
625A TRP* 2.9 32.4 + - + +
629A THR* 3.6 21.3 - - + +
656A ILE* 5.1 1.1 - - + -
669A VAL 2.9 17.7 + - - +
670A ILE 3.6 5.6 - - - +
672A THR* 1.3 79.3 - - - +
674A GLN* 1.3 56.1 + - - +
676A ALA 3.4 0.2 + - - -
677A MET* 3.0 15.9 + - - +
692A THR* 4.0 2.0 - - - +
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Residues in contact with GLN 674 (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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670A ILE 3.3 8.0 + - - +
671A GLU* 3.3 11.6 + - - +
672A THR 3.2 0.6 - - - -
673A ALA* 1.3 74.4 - - - +
675A GLU* 1.3 69.2 + - + +
677A MET* 3.2 3.6 + - - +
678A ARG* 3.1 48.3 + - + +
691A ASP* 2.9 28.4 + - - +
692A THR* 2.8 51.1 + - - +
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Residues in contact with GLU 675 (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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632A MET* 3.1 27.6 - - + +
636A LYS* 3.2 22.2 + - - -
671A GLU* 3.0 31.6 + - + +
672A THR* 3.3 9.5 + - - +
674A GLN* 1.3 80.1 - - + +
676A ALA* 1.3 61.9 + - - +
678A ARG* 3.3 7.6 + - - +
679A TRP* 3.0 21.1 + - - +
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Residues in contact with ALA 676 (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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625A TRP* 3.9 5.8 - - + -
628A LYS* 3.9 5.7 - - + +
629A THR* 3.3 43.7 - - - +
632A MET* 3.7 14.7 - - - -
672A THR 2.8 16.8 + - - +
673A ALA 3.7 1.3 - - - +
674A GLN 3.3 0.2 - - - -
675A GLU* 1.3 74.4 - - - +
677A MET* 1.3 56.9 + - - +
679A TRP* 3.2 6.2 + - - +
680A VAL* 2.9 31.2 + - - +
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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
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476A ALA* 3.8 27.4 - - + -
479A LEU* 5.2 2.0 - - + -
621A ILE* 3.9 26.5 - - + -
625A TRP* 3.6 38.7 - - + -
673A ALA 3.0 7.5 + - - +
674A GLN 3.2 6.5 + - - +
676A ALA* 1.3 72.9 - - - +
678A ARG* 1.3 66.4 + - - +
680A VAL* 3.0 7.4 + - - +
681A GLY* 3.0 18.7 + - - -
690A LEU* 3.6 38.5 - - + +
691A ASP* 4.0 2.7 - - - +
692A THR* 3.6 26.7 - - + -
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Residues in contact with ARG 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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674A GLN* 3.1 31.4 + - + +
675A GLU* 3.6 9.2 - - - +
677A MET* 1.3 76.2 - - - +
679A TRP* 1.3 63.9 + - - +
681A GLY* 3.2 2.9 + - - +
682A ASP* 3.0 25.3 + - - +
689A LEU* 3.7 41.0 - - - +
690A LEU* 2.9 26.2 + - - +
691A ASP* 2.7 20.6 + - - -
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Residues in contact with TRP 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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219A ARG* 5.4 5.8 - - - -
624A LEU* 4.2 23.1 - - + -
628A LYS* 3.8 47.8 - - + +
632A MET* 5.2 2.5 - - + -
675A GLU 3.0 14.5 + - - +
676A ALA* 3.3 13.5 - - - +
678A ARG* 1.3 78.5 - - - +
680A VAL* 1.3 59.3 + - + +
682A ASP* 3.3 10.0 + - - +
683A HIS* 2.7 71.3 + + + +
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Residues in contact with VAL 680 (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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621A ILE* 4.1 29.6 - - + +
624A LEU* 3.8 25.8 - - + +
625A TRP* 3.8 20.6 - - + +
628A LYS* 4.7 1.1 - - + -
676A ALA 2.9 18.0 + - - +
677A MET* 3.0 10.7 + - - +
679A TRP* 1.3 87.8 - - + +
681A GLY* 1.3 64.7 + - - +
683A HIS* 3.2 4.9 + - - +
684A TRP* 3.0 45.1 + - + +
690A LEU* 4.7 0.9 - - + -
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Residues in contact with GLY 681 (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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677A MET 3.0 12.0 + - - -
678A ARG* 3.2 4.0 + - - -
680A VAL* 1.3 77.6 - - - +
682A ASP* 1.3 60.0 + - - +
684A TRP 3.7 0.2 + - - -
685A ASN* 3.2 2.1 + - - -
686A PHE* 2.8 40.4 + - - +
688A CYS 5.6 0.2 - - - -
690A LEU* 3.8 24.4 - - - +
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Residues in contact with ASP 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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678A ARG 3.0 16.2 + - - +
679A TRP* 3.7 9.9 - - - +
681A GLY* 1.3 73.7 - - - +
683A HIS* 1.3 69.1 + - - +
685A ASN* 3.1 21.4 + - - +
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Residues in contact with HIS 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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212A GLU* 2.8 27.8 + - - -
624A LEU* 3.6 21.1 - - + +
679A TRP* 2.7 54.6 + + + +
680A VAL 3.4 5.2 - - - +
682A ASP* 1.3 79.1 + - - +
684A TRP* 1.3 81.3 + + - +
685A ASN* 3.6 7.4 + - - -
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Residues in contact with TRP 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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212A GLU* 3.1 19.6 + - - -
216A ILE* 3.7 27.1 - - + -
486A HIS* 4.6 3.3 + - - -
596A LEU* 3.4 50.7 + - + +
597A ASP* 3.8 12.8 - - + -
620A LEU* 3.6 36.6 - - + -
621A ILE* 4.0 8.3 - - + -
624A LEU* 3.6 20.0 - - + -
680A VAL* 3.0 25.4 + - + +
682A ASP 3.2 0.2 - - - -
683A HIS* 1.3 95.8 - + - +
685A ASN* 1.3 75.8 + - - +
686A PHE* 3.1 18.4 + - + -
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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