Contacts of the helix formed by residues 621 - 640 (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 ASP 621 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6191 ASN 3.1 12.3 + - - +
6201 MET* 1.3 73.5 - - - +
6221 GLU* 1.3 67.3 + - - +
6231 TYR 3.1 4.4 + - - +
6241 VAL* 3.5 6.1 + - - +
6251 ARG* 3.5 11.6 + - - -
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Residues in contact with GLU 622 (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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6201 MET 3.2 5.5 + - - -
6211 ASP* 1.3 73.4 - - - +
6231 TYR* 1.3 66.9 + - - +
6251 ARG* 3.1 3.3 + - - +
6261 ASN* 2.9 18.2 + - - -
156G U 5.5 8.5 - - - -
157G U 6.1 4.0 - - - -
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Residues in contact with TYR 623 (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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6211 ASP* 3.1 1.8 - - - +
6221 GLU* 1.3 79.8 - - - +
6241 VAL* 1.3 62.6 + - - +
6261 ASN* 2.8 10.1 + - - +
6271 THR* 3.0 11.8 + - - -
156G U 6.4 2.0 - - - -
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Residues in contact with VAL 624 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6161 ASP* 4.7 7.4 - - - +
6211 ASP* 3.5 7.8 + - - +
6221 GLU 3.3 0.4 - - - -
6231 TYR* 1.3 73.5 - - - +
6251 ARG* 1.3 64.7 + - - +
6271 THR* 4.8 1.3 - - - +
6281 THR* 2.8 18.0 + - - -
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Residues in contact with ARG 625 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6161 ASP 4.3 14.7 + - - -
6171 ILE* 5.0 7.0 - - - +
6191 ASN 5.6 0.4 - - - -
6211 ASP 3.5 8.7 + - - -
6221 GLU* 3.1 7.1 + - - +
6241 VAL* 1.3 73.9 - - - +
6261 ASN* 1.3 54.9 + - - +
6281 THR* 2.5 27.0 + - - +
6291 ALA 2.8 11.3 + - - -
6631 THR* 6.2 5.6 - - - +
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Residues in contact with ASN 626 (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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6221 GLU 2.9 9.6 + - - -
6231 TYR* 2.8 12.0 + - - +
6251 ARG* 1.3 69.8 - - - +
6271 THR* 1.3 67.0 + - - +
6291 ALA* 3.1 8.8 + - - -
6301 ARG 3.2 7.3 + - - -
156G U 6.1 2.2 - - - -
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Residues in contact with THR 627 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5791 GLU* 5.5 13.0 - - - +
6231 TYR 3.0 11.3 + - - -
6241 VAL* 4.2 1.1 - - - +
6261 ASN* 1.3 73.9 - - - +
6281 THR* 1.3 54.5 + - - +
6301 ARG* 2.5 26.9 + - - +
6311 ALA* 2.9 9.9 + - - -
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Residues in contact with THR 628 (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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6161 ASP 6.4 1.1 - - - -
6241 VAL 2.8 14.5 + - - -
6251 ARG* 2.5 17.2 + - - +
6271 THR* 1.3 63.3 - - - +
6291 ALA* 1.3 68.2 + - - +
6311 ALA* 3.3 4.2 + - - +
6321 PHE* 3.1 13.5 + - - -
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Residues in contact with ALA 629 (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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6251 ARG 2.8 10.9 + - - -
6261 ASN 3.1 4.7 + - - -
6281 THR* 1.3 74.1 - - - +
6301 ARG* 1.3 55.4 + - - +
6321 PHE* 2.4 32.0 + - - +
6331 ALA 2.9 7.4 + - - -
6631 THR* 6.0 1.8 - - - +
6661 LYS 5.7 0.7 - - - -
6671 ILE* 4.8 20.3 - - - +
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Residues in contact with ARG 630 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6261 ASN 3.2 7.3 + - - -
6271 THR* 2.5 14.9 + - - +
6291 ALA* 1.3 68.2 - - - +
6311 ALA* 1.3 64.4 + - - +
6331 ALA* 3.1 5.2 + - - +
6341 VAL* 3.0 15.1 + - - -
6701 GLN* 5.9 5.8 - - - +
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Residues in contact with ALA 631 (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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6271 THR 2.9 9.4 + - - -
6281 THR* 3.5 5.4 - - - +
6291 ALA 2.6 4.6 + - - -
6301 ARG* 1.3 72.5 - - - +
6321 PHE* 1.3 52.9 + - - +
6341 VAL* 2.5 28.9 + - - +
6351 VAL* 3.0 10.4 + - - -
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Residues in contact with PHE 632 (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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6281 THR 3.1 7.4 + - - -
6291 ALA* 2.4 15.7 + - - +
6311 ALA* 1.3 67.9 - - - +
6331 ALA* 1.3 65.0 + - - +
6351 VAL* 4.4 3.6 - - - +
6361 ALA* 3.0 17.7 + - - -
6671 ILE* 6.3 0.9 - - - -
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Residues in contact with ALA 633 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6291 ALA 2.9 8.7 + - - -
6301 ARG* 3.1 6.9 + - - +
6311 ALA 2.7 5.7 + - - -
6321 PHE* 1.3 78.4 - - - +
6341 VAL* 1.3 60.8 + - - +
6361 ALA* 3.0 1.4 + - - -
6371 SER* 3.0 16.1 + - - -
6671 ILE* 5.4 4.6 + - - +
6701 GLN 4.8 4.7 - - - -
6711 ILE* 4.5 25.1 - - - +
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Residues in contact with VAL 634 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5941 ARG* 6.1 2.5 - - - +
5971 ILE 6.0 0.9 - - - -
5981 SER* 5.4 10.8 - - - +
6301 ARG 3.0 8.1 + - - -
6311 ALA* 2.5 14.0 + - - +
6331 ALA* 1.3 69.5 - - - +
6351 VAL* 1.3 53.7 + - - +
6371 SER* 2.6 25.8 + - - +
6381 ALA* 2.9 8.7 + - - -
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Residues in contact with VAL 635 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5971 ILE 5.4 7.4 + - - -
5981 SER* 5.7 1.6 - - - +
6011 ALA* 5.5 9.6 - - - +
6311 ALA 3.0 11.0 + - - -
6321 PHE* 4.1 2.9 - - - +
6341 VAL* 1.3 74.1 - - - +
6361 ALA* 1.3 56.1 + - - +
6381 ALA* 3.2 3.1 + - - +
6391 LEU* 2.9 25.1 + - - -
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Residues in contact with ALA 636 (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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6321 PHE 3.0 13.0 + - - -
6331 ALA 3.4 4.5 - - - -
6341 VAL 2.7 2.0 + - - -
6351 VAL* 1.3 75.9 - - - +
6371 SER* 1.3 63.5 + - - +
6381 ALA 3.0 1.3 - - - -
6391 LEU 4.4 0.4 - - - +
6401 GLY* 2.8 36.3 + - - -
6411 ILE* 4.1 2.5 + - - +
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Residues in contact with SER 637 (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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6331 ALA 3.0 8.4 + - - -
6341 VAL* 2.6 14.3 + - - +
6361 ALA* 1.3 74.1 - - - +
6381 ALA* 1.3 61.3 + - - +
6401 GLY* 4.2 2.3 + - - -
6751 MET* 6.2 3.8 - - - +
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Residues in contact with ALA 638 (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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5981 SER* 5.6 8.5 - - - +
6021 LYS* 5.7 9.6 - - - +
6341 VAL 2.9 10.8 + - - -
6351 VAL* 3.2 4.7 + - - +
6371 SER* 1.3 81.3 - - - +
6391 LEU* 1.3 57.1 + - - +
6401 GLY 3.3 3.5 + - - -
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Residues in contact with LEU 639 (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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6021 LYS* 6.2 0.4 - - - +
6351 VAL 2.9 15.8 + - - -
6361 ALA 3.8 0.2 - - - -
6381 ALA* 1.3 71.4 - - - +
6401 GLY* 1.3 67.1 + - - +
6431 SER* 4.5 10.9 + - - -
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Residues in contact with GLY 640 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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