Contacts of the helix formed by residues 996 - 1004 (chain A) in PDB entry 6CIM
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 996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A LEU* 4.5 16.2 - - - +
569A ASP* 3.1 20.6 + - - -
653A LYS* 3.8 4.9 - - - +
992A TRP* 3.3 9.0 + - - -
993A LEU* 3.2 13.3 + - - +
995A THR* 1.3 76.1 - - - +
997A LYS* 1.3 63.0 + - - +
998A TYR* 4.1 1.0 - - - +
999A LEU* 3.4 35.8 + - - +
1000A GLN* 3.2 22.2 + - - +
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Residues in contact with LYS 997 (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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569A ASP* 2.5 22.2 + - - +
570A MET* 3.5 37.0 - - + -
573A ASP* 4.4 22.2 + - - +
641A PHE* 4.1 13.0 - - + -
643A GLU* 3.3 32.6 + - - -
644A PRO* 4.4 8.7 - - - +
651A CYS* 4.5 11.6 - - - +
653A LYS* 6.1 0.4 - - - +
995A THR 3.4 3.8 + - - +
996A SER* 1.3 69.3 - - - +
998A TYR* 1.3 65.4 + - - +
1000A GLN* 3.7 20.6 + - - +
1001A LYS* 2.9 24.4 + - - +
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Residues in contact with TYR 998 (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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465A ALA* 4.1 22.2 - - + +
509A VAL* 6.4 1.6 - - + -
510A LEU* 3.5 26.2 - - + -
569A ASP* 2.9 25.3 + - - +
572A GLU* 4.2 26.5 - - + -
996A SER* 4.1 1.3 - - - +
997A LYS* 1.3 75.2 - - - +
999A LEU* 1.3 73.6 + - + +
1001A LYS* 3.0 19.6 + - + +
1002A PHE* 3.2 36.7 + + - -
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Residues in contact with LEU 999 (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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465A ALA 4.3 10.5 - - - +
468A LEU* 4.1 27.1 - - + +
469A ALA* 3.7 30.2 - - + +
472A VAL* 4.6 4.9 - - + -
473A ASN* 6.1 2.0 - - - +
510A LEU* 3.6 24.7 - - + -
993A LEU* 3.9 22.4 - - + +
996A SER* 3.4 21.4 + - - +
998A TYR* 1.3 89.1 - - + +
1000A GLN* 1.3 58.1 + - + +
1002A PHE* 2.9 23.4 + - + +
1003A MET* 2.9 17.4 + - + +
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Residues in contact with GLN1000 (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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473A ASN* 5.2 7.6 - - - +
650A LEU* 3.0 56.7 + - + +
651A CYS* 6.1 0.2 - - - +
994A TYR 3.4 16.4 + - - +
995A THR 3.1 12.0 + - - -
996A SER 3.2 11.8 + - - +
997A LYS* 3.7 23.1 + - - +
998A TYR 3.3 0.6 - - - -
999A LEU* 1.3 76.9 - - + +
1001A LYS* 1.3 64.3 + - - +
1003A MET* 3.1 9.2 + - - +
1004A ASN* 2.8 38.6 + - - +
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Residues in contact with LYS1001 (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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572A GLU* 5.1 13.5 - - - +
573A ASP* 5.6 8.8 + - - +
576A GLU* 5.2 7.5 + - - -
997A LYS 2.9 13.2 + - - +
998A TYR* 3.2 17.3 - - + +
1000A GLN* 1.3 75.4 - - - +
1002A PHE* 1.3 64.7 + - + +
1004A ASN* 3.1 16.3 + - + +
1005A ALA* 3.4 10.0 + - - -
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Residues in contact with PHE1002 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A GLN* 6.0 1.6 - - + -
465A ALA* 4.0 16.6 - - + -
466A VAL* 3.5 34.8 - - + -
469A ALA* 4.0 17.0 - - + -
998A TYR* 3.2 53.4 + + - -
999A LEU* 2.9 15.2 + - + +
1001A LYS* 1.3 78.7 - - + +
1003A MET* 1.3 62.7 + - - +
1005A ALA* 3.3 20.3 + - - +
487C THR* 3.7 13.1 - - + +
491C ILE* 3.5 17.2 - - + +
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Residues in contact with MET1003 (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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469A ALA* 3.7 30.5 - - + +
470A ILE* 3.9 17.9 - - + -
473A ASN* 3.9 36.6 - - + +
474A THR* 5.1 3.6 - - + -
999A LEU* 2.9 20.2 + - + +
1000A GLN* 3.1 8.4 + - - +
1002A PHE* 1.3 76.3 - - - +
1004A ASN* 1.3 65.2 + - - +
1005A ALA 3.5 0.9 - - - -
1006A HIS* 3.6 13.9 - - - -
483C LYS* 4.3 23.6 - - + +
484C MET 5.3 0.2 - - - +
486C ARG* 4.7 5.9 + - - +
487C THR* 3.6 30.2 + - - +
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Residues in contact with ASN1004 (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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1000A GLN* 2.8 31.6 + - - +
1001A LYS* 3.1 8.7 + - + +
1003A MET* 1.3 85.7 - - - +
1005A ALA* 1.3 61.7 + - - +
1006A HIS* 3.2 13.5 + - - -
1007A ASN* 3.1 30.1 + - + +
486C ARG* 5.4 2.9 + - - -
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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