Contacts of the helix formed by residues 640 - 652 (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 GLY 640 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6361 ALA* 2.8 22.2 + - - +
6371 SER 4.2 2.2 + - - -
6381 ALA 3.3 4.4 + - - -
6391 LEU* 1.3 84.5 - - - +
6411 ILE* 1.3 69.9 + - - +
6421 PRO 3.4 1.6 - - - -
6431 SER 3.8 0.6 + - - -
6441 LEU* 3.7 7.1 + - - -
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Residues in contact with ILE 641 (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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6361 ALA* 4.1 5.0 + - - +
6401 GLY* 1.3 71.4 - - - +
6421 PRO* 1.3 53.6 - - - +
6441 LEU* 2.4 31.5 + - - -
6451 LEU* 3.0 9.4 + - - -
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Residues in contact with PRO 642 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6401 GLY* 3.4 0.8 - - - -
6411 ILE* 1.3 70.3 - - - +
6431 SER* 1.3 67.8 + - - +
6441 LEU 3.3 0.3 + - - -
6451 LEU* 3.6 9.5 + - - +
6461 PRO 4.7 1.9 - - - -
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Residues in contact with SER 643 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6391 LEU 4.5 7.5 + - - -
6401 GLY 3.8 6.6 + - - -
6411 ILE 3.0 1.6 + - - -
6421 PRO* 1.3 78.7 - - - +
6441 LEU* 1.3 58.4 + - - +
6461 PRO 4.5 2.9 - - - -
6471 PHE 5.3 0.2 + - - -
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Residues in contact with LEU 644 (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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6401 GLY 3.7 5.4 + - - -
6411 ILE 2.4 18.4 + - - -
6431 SER* 1.3 73.3 - - - +
6451 LEU* 1.3 66.1 + - - +
6461 PRO 3.4 0.4 - - - -
6471 PHE* 3.1 11.9 + - - -
6481 LEU 3.4 7.3 + - - -
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Residues in contact with LEU 645 (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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6411 ILE 3.0 10.8 + - - -
6421 PRO* 3.6 6.7 + - - -
6431 SER 3.4 2.0 - - - -
6441 LEU* 1.3 74.5 - - - +
6461 PRO* 1.3 66.5 - - - +
6481 LEU* 2.6 17.9 + - - +
6491 LYS* 2.9 11.5 + - - +
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Residues in contact with PRO 646 (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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2121 PRO 4.8 5.9 - - - +
2131 LYS* 4.9 5.5 - - - -
2161 SER* 4.9 17.6 - - - +
6421 PRO 4.7 2.4 - - - -
6431 SER 4.5 3.6 - - - -
6441 LEU 3.3 1.2 - - - -
6451 LEU* 1.3 71.8 - - - +
6471 PHE* 1.3 57.3 + - - +
6491 LYS* 3.8 2.6 - - - +
6501 ALA* 2.9 24.4 + - - -
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Residues in contact with PHE 647 (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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2091 GLY 5.7 0.3 - - - +
2131 LYS* 5.3 8.2 - - - +
6431 SER 5.3 0.2 + - - -
6441 LEU 3.1 8.9 + - - -
6451 LEU 2.6 4.4 + - - -
6461 PRO* 1.3 70.3 - - - +
6481 LEU* 1.3 67.3 + - - +
6501 ALA* 2.7 12.3 + - - -
6511 VAL* 2.9 8.0 + - - -
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Residues in contact with LEU 648 (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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6441 LEU 3.4 6.1 + - - -
6451 LEU* 2.6 11.4 + - - +
6471 PHE* 1.3 67.8 - - - +
6491 LYS* 1.3 52.2 + - - +
6501 ALA 2.7 1.2 + - - -
6511 VAL* 2.1 37.0 + - - +
6521 CYS 3.1 5.5 + - - -
6641 GLY* 6.1 2.9 - - - -
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Residues in contact with LYS 649 (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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6451 LEU* 2.9 15.2 + - - +
6461 PRO* 3.8 3.1 - - - -
6481 LEU* 1.3 70.2 - - - +
6501 ALA* 1.3 62.2 + - - +
6521 CYS* 3.9 3.5 + - - +
6531 LYS* 3.7 12.5 + - - -
6891 ILE* 5.7 8.5 - - - +
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Residues in contact with ALA 650 (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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2091 GLY* 5.2 10.3 - - - -
2121 PRO* 5.0 18.6 - - - +
2131 LYS 5.4 0.7 - - - +
6461 PRO 2.9 11.6 + - - -
6471 PHE* 2.7 10.3 + - - +
6481 LEU 2.7 0.8 + - - -
6491 LYS* 1.3 75.4 - - - +
6511 VAL* 1.3 68.0 + - - +
6531 LYS* 3.0 12.1 + - - -
6541 SER* 3.2 8.1 + - - -
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Residues in contact with VAL 651 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2091 GLY* 5.6 4.7 - - - -
6471 PHE 2.9 7.4 + - - -
6481 LEU* 2.1 21.1 + - - +
6501 ALA* 1.3 67.0 - - - +
6521 CYS* 1.3 51.7 + - - +
6541 SER* 2.5 31.7 + - - +
6601 ALA 6.1 0.7 - - - -
6611 ARG* 5.1 8.4 + - - -
6641 GLY* 5.8 4.9 - - - -
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Residues in contact with CYS 652 (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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6481 LEU 3.1 8.9 + - - -
6491 LYS* 3.9 3.1 + - - +
6501 ALA 3.4 0.2 - - - -
6511 VAL* 1.3 72.6 - - - +
6531 LYS* 1.3 56.6 + - - +
6541 SER 3.4 2.8 - - - +
6611 ARG* 5.0 13.9 - - - +
6641 GLY* 5.5 6.3 - - - -
6651 ILE 6.0 1.1 - - - +
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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