Contacts of the helix formed by residues 1028 - 1046 (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 HIS1028 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9871 PRO* 6.5 0.4 - - - -
10261 ASN* 2.4 21.2 + - - +
10271 ARG* 1.3 71.9 + - - +
10291 GLU* 1.3 67.9 + - - +
10301 LYS 3.7 0.2 - - - -
10311 VAL* 4.1 3.6 + - - -
10321 GLN* 3.6 10.6 + - - -
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Residues in contact with GLU1029 (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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10271 ARG 4.3 1.8 - - - -
10281 HIS* 1.3 68.2 - - - +
10301 LYS* 1.3 58.4 + - - +
10311 VAL 3.0 2.2 - - - -
10321 GLN* 2.5 30.5 + - - -
10331 GLU* 3.0 8.2 + - - -
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Residues in contact with LYS1030 (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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9871 PRO 6.0 0.9 - - - -
9911 GLY* 4.4 13.8 - - - -
10281 HIS 3.7 0.4 - - - -
10291 GLU* 1.3 73.6 - - - +
10311 VAL* 1.3 64.5 + - - +
10331 GLU* 3.4 3.2 + - - +
10341 ASN* 3.0 17.5 + - - -
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Residues in contact with VAL1031 (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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9871 PRO* 5.1 6.7 + - - +
9901 LEU 5.7 0.7 - - - -
9911 GLY* 4.5 13.6 - - - +
10281 HIS 4.1 4.1 + - - -
10291 GLU 2.8 1.8 + - - +
10301 LYS* 1.3 77.5 - - - +
10321 GLN* 1.3 64.2 + - - +
10331 GLU 2.8 1.9 + - - -
10341 ASN* 3.7 0.2 - - - -
10351 CYS* 2.8 23.3 + - - -
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Residues in contact with GLN1032 (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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10241 LEU* 6.4 1.8 - - - +
10261 ASN* 6.2 1.4 - - - +
10281 HIS 3.6 8.0 + - - -
10291 GLU 2.5 13.6 + - - -
10311 VAL* 1.3 68.4 - - - +
10331 GLU* 1.3 63.8 + - - +
10351 CYS* 5.2 0.7 - - - +
10361 ILE* 3.0 18.9 + - - +
10731 ILE* 5.9 2.7 - - - -
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Residues in contact with GLU1033 (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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10291 GLU 3.0 8.9 + - - -
10301 LYS* 3.7 4.0 - - - +
10311 VAL 2.8 1.6 + - - -
10321 GLN* 1.3 81.0 - - - +
10341 ASN* 1.3 63.4 + - - +
10361 ILE* 3.9 0.2 - - - -
10371 ASP* 3.0 18.0 + - - -
10731 ILE* 5.7 8.5 - - - +
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Residues in contact with ASN1034 (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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9911 GLY* 5.4 8.1 - - - -
9941 LEU* 5.7 7.1 - - - +
9951 GLY* 5.4 9.6 - - - +
10301 LYS 3.0 10.6 + - - -
10311 VAL 2.9 6.8 + - - -
10331 GLU* 1.3 71.2 - - - +
10351 CYS* 1.3 66.6 + - - +
10371 ASP* 3.5 2.4 + - - +
10381 LEU* 2.9 16.1 + - - -
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Residues in contact with CYS1035 (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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10311 VAL 2.8 15.4 + - - -
10321 GLN* 4.0 1.1 - - - +
10341 ASN* 1.3 73.9 - - - +
10361 ILE* 1.3 54.8 + - - +
10381 LEU* 2.4 27.7 + - - +
10391 VAL* 2.9 10.7 + - - -
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Residues in contact with ILE1036 (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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10321 GLN 3.0 15.8 + - - -
10331 GLU 3.9 0.2 - - - -
10351 CYS* 1.3 72.3 - - - +
10371 ASP* 1.3 62.1 + - - +
10391 VAL* 3.9 2.4 - - - +
10401 GLY* 2.9 21.0 + - - +
10761 ALA* 5.5 8.5 - - - +
10771 THR* 6.3 2.7 - - - +
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Residues in contact with ASP1037 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10331 GLU 3.0 13.0 + - - -
10341 ASN* 3.7 4.5 - - - +
10351 CYS 2.9 0.2 + - - -
10361 ILE* 1.3 74.9 - - - +
10381 LEU* 1.3 61.6 + - - +
10401 GLY* 3.0 11.5 + - - -
10411 ARG* 3.0 11.6 + - - -
10761 ALA* 6.5 1.1 - - - +
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Residues in contact with LEU1038 (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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9981 LYS* 5.6 9.6 - - - +
10341 ASN 2.9 9.9 + - - -
10351 CYS* 2.4 14.4 + - - +
10371 ASP* 1.3 67.4 - - - +
10391 VAL* 1.3 66.8 + - - +
10411 ARG* 2.8 15.2 + - - +
10421 ILE* 3.0 10.0 + - - -
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Residues in contact with VAL1039 (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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10351 CYS 2.9 14.5 + - - -
10361 ILE* 4.0 2.7 - - - +
10381 LEU* 1.3 69.4 - - - +
10401 GLY* 1.3 63.2 + - - +
10421 ILE* 3.8 1.2 - - - +
10431 ALA* 2.8 23.9 + - - -
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Residues in contact with GLY1040 (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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10361 ILE 2.9 16.2 + - - -
10371 ASP 3.3 4.5 - - - -
10381 LEU 2.8 0.8 + - - -
10391 VAL* 1.3 76.6 - - - +
10411 ARG* 1.3 62.8 + - - +
10421 ILE 3.0 0.3 + - - -
10431 ALA* 3.7 0.6 - - - -
10441 ASP* 2.9 22.2 + - - -
10761 ALA 6.1 0.4 - - - -
10801 THR* 5.0 16.8 - - - -
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Residues in contact with ARG1041 (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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10371 ASP 3.0 8.2 + - - -
10381 LEU* 2.8 10.4 + - - +
10401 GLY* 1.3 71.8 - - - +
10421 ILE* 1.3 58.3 + - - +
10441 ASP* 3.3 1.5 + - - +
10451 ARG* 2.9 25.3 + - - -
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Residues in contact with ILE1042 (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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10381 LEU 3.0 10.8 + - - -
10391 VAL* 3.9 1.8 - - - +
10411 ARG* 1.3 77.8 - - - +
10431 ALA* 1.3 61.3 + - - +
10441 ASP 3.1 0.2 - - - -
10451 ARG* 5.1 0.2 - - - +
10461 GLY* 3.1 25.8 + - - +
10471 ALA 3.3 6.4 + - - -
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Residues in contact with ALA1043 (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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10391 VAL 2.8 16.0 + - - -
10401 GLY 3.7 0.9 - - - -
10421 ILE* 1.3 75.2 - - - +
10441 ASP* 1.3 60.8 + - - +
10471 ALA* 4.2 16.3 - - - +
10831 TYR* 4.3 19.2 - - - +
10841 ILE* 4.8 3.8 + - - +
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Residues in contact with ASP1044 (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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10401 GLY 2.9 13.7 + - - -
10411 ARG* 3.7 3.4 - - - +
10431 ALA* 1.3 80.9 - - - +
10451 ARG* 1.3 64.0 + - - +
10461 GLY 4.8 0.9 - - - -
10471 ALA* 5.2 0.3 - - - -
10831 TYR* 5.3 8.5 - - - +
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Residues in contact with ARG1045 (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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10411 ARG 2.9 15.0 + - - -
10421 ILE* 5.1 0.2 - - - +
10441 ASP* 1.3 78.3 - - - +
10461 GLY* 1.3 69.3 + - - +
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Residues in contact with GLY1046 (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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10061 MET* 6.1 5.2 - - - -
10421 ILE* 3.1 8.6 + - - +
10441 ASP 4.8 0.3 - - - +
10451 ARG* 1.3 78.1 - - - +
10471 ALA* 1.3 53.8 + - - +
10481 GLU* 2.5 20.5 + - - -
10491 TYR 4.5 2.7 - - - -
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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
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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