Contacts of the helix formed by residues 657 - 676 (chain 1) in PDB entry 6AH0
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 657 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6541 SER 3.9 14.9 - - - +
6551 LYS 3.5 0.9 - - - -
6561 LYS* 1.3 75.2 - - - +
6581 TRP* 1.3 64.7 + - - +
6591 GLN 3.5 2.5 - - - +
6601 ALA* 4.3 5.3 + - - -
6611 ARG 4.4 3.3 + - - -
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Residues in contact with TRP 658 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6571 SER* 1.3 71.0 - - - +
6591 GLN* 1.3 55.6 + - - +
6601 ALA 3.0 2.9 - - - -
6611 ARG* 2.3 35.0 + - - +
6621 HIS* 2.8 9.0 + - - -
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Residues in contact with GLN 659 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6171 ILE 4.8 7.3 - - - +
6181 ASP* 5.6 2.2 - - - +
6571 SER* 3.5 1.6 - - - +
6581 TRP* 1.3 72.7 - - - +
6601 ALA* 1.3 66.5 + - - +
6621 HIS* 3.2 4.2 + - - +
6631 THR* 2.9 13.0 + - - -
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Residues in contact with ALA 660 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6171 ILE* 4.7 15.0 + - - +
6181 ASP* 5.2 4.4 - - - +
6511 VAL 5.8 1.6 - - - -
6571 SER 4.3 4.8 + - - -
6581 TRP 2.8 3.4 + - - -
6591 GLN* 1.3 70.0 - - - +
6611 ARG* 1.3 53.0 + - - +
6631 THR* 2.2 33.6 + - - +
6641 GLY* 2.8 10.8 + - - -
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Residues in contact with ARG 661 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6511 VAL 5.1 4.9 + - - -
6521 CYS* 5.0 16.6 - - - +
6541 SER 5.8 2.4 + - - -
6571 SER 4.4 3.2 + - - -
6581 TRP* 2.3 19.0 + - - +
6601 ALA* 1.3 67.3 - - - +
6621 HIS* 1.3 60.3 + - - +
6641 GLY* 4.2 3.6 - - - +
6651 ILE* 2.9 23.3 + - - +
7011 VAL* 5.9 1.8 - - - -
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Residues in contact with HIS 662 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6581 TRP 2.8 11.0 + - - -
6591 GLN* 3.2 5.4 + - - +
6601 ALA 2.7 3.6 + - - -
6611 ARG* 1.3 73.5 - - - +
6631 THR* 1.3 66.2 + - - +
6651 ILE* 3.6 0.5 + - - -
6661 LYS* 3.0 15.2 + - - -
7011 VAL* 5.1 14.6 - - - +
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Residues in contact with THR 663 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6171 ILE 6.1 0.9 - - - -
6251 ARG* 6.2 5.4 - - - +
6591 GLN 2.9 8.5 + - - -
6601 ALA* 2.2 18.7 + - - +
6621 HIS* 1.3 67.3 - - - +
6641 GLY* 1.3 54.4 + - - +
6661 LYS* 2.4 29.7 + - - +
6671 ILE* 2.9 9.3 + - - -
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Residues in contact with GLY 664 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6481 LEU* 6.1 2.7 - - - -
6511 VAL* 5.8 3.1 - - - -
6521 CYS* 5.5 9.6 - - - -
6601 ALA 2.8 14.7 + - - -
6611 ARG* 3.2 4.2 + - - -
6631 THR* 1.3 69.8 - - - +
6651 ILE* 1.3 65.8 + - - +
6671 ILE* 3.1 4.5 + - - -
6681 VAL* 3.0 14.6 + - - -
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Residues in contact with ILE 665 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6521 CYS* 6.0 1.2 - - - +
6611 ARG 2.9 15.9 + - - -
6621 HIS 4.0 0.4 - - - -
6631 THR 2.7 3.4 + - - -
6641 GLY* 1.3 73.0 - - - +
6661 LYS* 1.3 54.7 + - - +
6681 VAL* 2.5 27.1 + - - +
6691 GLN 3.1 6.6 + - - -
7041 ILE 6.0 4.3 - - - -
7051 SER* 5.9 6.3 - - - +
7081 ALA* 6.0 1.0 - - - -
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Residues in contact with LYS 666 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6291 ALA* 5.7 1.1 - - - -
6621 HIS 3.0 11.8 + - - -
6631 THR* 2.4 16.9 + - - +
6651 ILE* 1.3 67.2 - - - +
6671 ILE* 1.3 53.0 + - - +
6691 GLN* 2.6 25.3 + - - +
6701 GLN 2.9 11.6 + - - -
7041 ILE* 6.1 2.3 - - - +
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Residues in contact with ILE 667 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6291 ALA* 4.8 20.7 - - - +
6321 PHE 6.3 0.4 - - - -
6331 ALA* 5.4 4.9 - - - +
6631 THR 2.9 9.4 + - - -
6641 GLY* 3.4 6.7 - - - -
6661 LYS* 1.3 73.5 - - - +
6681 VAL* 1.3 66.2 + - - +
6691 GLN 2.9 0.3 + - - -
6701 GLN* 3.1 1.3 + - - +
6711 ILE* 2.9 22.5 + - - -
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Residues in contact with VAL 668 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6641 GLY 3.0 8.6 + - - -
6651 ILE* 2.5 15.6 + - - +
6671 ILE* 1.3 71.2 - - - +
6691 GLN* 1.3 65.5 + - - +
6711 ILE* 3.3 2.0 + - - +
6721 ALA* 2.9 14.0 + - - -
7081 ALA* 5.9 0.4 - - - -
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Residues in contact with GLN 669 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6651 ILE 3.1 5.9 + - - -
6661 LYS* 2.6 15.4 + - - +
6681 VAL* 1.3 70.5 - - - +
6701 GLN* 1.3 52.5 + - - +
6721 ALA* 2.2 36.9 + - - +
6731 ILE 2.9 3.9 + - - -
7081 ALA* 4.8 19.0 - - - +
7111 ALA* 6.4 1.1 - - - +
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Residues in contact with GLN 670 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6301 ARG* 5.9 6.3 - - - +
6331 ALA* 4.8 9.8 - - - +
6661 LYS 2.9 14.7 + - - -
6671 ILE* 3.1 1.5 + - - +
6691 GLN* 1.3 70.3 - - - +
6711 ILE* 1.3 60.8 + - - +
6731 ILE* 3.8 3.5 - - - +
6741 LEU* 2.9 21.7 + - - -
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Residues in contact with ILE 671 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6331 ALA* 4.5 15.7 - - - +
6671 ILE 2.9 12.8 + - - -
6681 VAL* 3.5 4.9 - - - +
6691 GLN 2.7 0.6 + - - -
6701 GLN* 1.3 73.3 - - - +
6721 ALA* 1.3 67.4 + - - +
6751 MET* 2.9 23.7 + - - +
6761 GLY 4.0 0.2 + - - -
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Residues in contact with ALA 672 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6681 VAL 2.9 9.0 + - - -
6691 GLN* 2.2 20.2 + - - +
6711 ILE* 1.3 66.8 - - - +
6731 ILE* 1.3 62.4 + - - +
6761 GLY* 2.9 25.1 + - - +
7111 ALA 5.5 5.8 - - - -
7121 LEU* 5.4 13.2 - - - +
7151 ALA* 5.9 1.4 - - - -
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Residues in contact with ILE 673 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6691 GLN 2.9 9.5 + - - -
6701 GLN* 3.3 3.9 + - - +
6721 ALA* 1.3 77.9 - - - +
6741 LEU* 1.3 65.4 + - - +
6761 GLY* 3.5 6.6 + - - -
7111 ALA* 6.0 0.8 - - - +
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Residues in contact with LEU 674 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6701 GLN 2.9 15.9 + - - -
6711 ILE* 5.3 0.2 - - - +
6731 ILE* 1.3 79.5 - - - +
6751 MET* 1.3 62.8 + - - +
6761 GLY* 3.0 1.2 + - - -
956 LYS 6.0 4.6 - - - -
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Residues in contact with MET 675 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6371 SER* 6.2 4.0 - - - +
6711 ILE* 2.9 15.1 + - - +
6741 LEU* 1.3 71.2 - - - +
6761 GLY* 1.3 67.3 + - - +
6771 CYS 3.3 0.7 + - - -
6781 ALA* 3.1 13.5 + - - -
6791 ILE* 4.5 4.7 - - - +
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Residues in contact with GLY 676 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6711 ILE 4.0 0.4 + - - -
6721 ALA* 2.9 22.2 + - - +
6731 ILE 3.7 7.6 - - - -
6741 LEU 3.0 2.8 + - - -
6751 MET* 1.3 75.3 - - - +
6771 CYS* 1.3 53.0 + - - -
6781 ALA 2.6 0.2 + - - -
6791 ILE* 2.5 33.0 + - - +
7151 ALA* 4.6 14.7 - - - +
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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
------------------------------------------------------------
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