Contacts of the helix formed by residues 928 - 942 (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 TYR 928 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9251 VAL 2.9 12.4 + - - -
9261 LYS 2.7 6.3 + - - -
9271 PRO* 1.3 76.5 - - - +
9291 LEU* 1.3 67.8 + - - +
9301 PRO 3.4 0.2 - - - -
9311 GLN* 3.1 11.4 + - - -
9321 ILE* 3.2 7.3 + - - -
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Residues in contact with LEU 929 (chain 1).
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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9251 VAL 4.0 2.8 + - - -
9261 LYS* 3.2 12.0 + - - +
9281 TYR* 1.3 74.1 - - - +
9301 PRO* 1.3 55.0 - - - +
9321 ILE* 2.3 31.9 + - - +
9331 CYS 2.9 10.7 + - - +
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Residues in contact with PRO 930 (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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9261 LYS 5.2 0.2 - - - -
9271 PRO 4.8 3.2 - - - -
9281 TYR 3.2 1.0 - - - -
9291 LEU* 1.3 71.9 - - - -
9311 GLN* 1.3 56.6 + - - +
9331 CYS* 4.6 1.3 - - - +
9341 GLY* 2.8 28.8 + - - +
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Residues in contact with GLN 931 (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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9271 PRO 5.6 0.4 + - - -
9281 TYR 3.1 7.3 + - - -
9291 LEU 2.6 4.4 + - - -
9301 PRO* 1.3 71.0 - - - +
9321 ILE* 1.3 67.8 + - - +
9341 GLY* 3.7 0.5 - - - -
9351 THR* 3.1 14.7 + - - -
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Residues in contact with ILE 932 (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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9281 TYR 3.2 7.0 + - - -
9291 LEU* 2.3 17.9 + - - +
9311 GLN* 1.3 65.5 - - - +
9331 CYS* 1.3 53.2 + - - +
9351 THR* 2.6 28.8 + - - -
9361 VAL* 2.8 9.0 + - - -
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Residues in contact with CYS 933 (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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9291 LEU* 2.9 13.1 + - - +
9301 PRO* 3.6 1.1 + - - -
9321 ILE* 1.3 69.9 - - - +
9341 GLY* 1.3 64.0 + - - +
9361 VAL* 3.5 5.3 - - - +
9371 LEU* 2.9 20.6 + - - -
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Residues in contact with GLY 934 (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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9301 PRO 2.8 20.1 + - - -
9311 GLN* 3.7 1.1 - - - -
9321 ILE 2.7 1.2 + - - -
9331 CYS* 1.3 77.7 - - - +
9351 THR* 1.3 62.4 + - - -
9371 LEU* 3.2 0.9 + - - -
9381 TRP* 2.9 19.1 + - - -
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Residues in contact with THR 935 (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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9311 GLN 3.1 9.4 + - - -
9321 ILE 2.6 12.1 + - - -
9341 GLY* 1.3 68.7 - - - -
9361 VAL* 1.3 66.1 + - - +
9381 TRP* 3.0 2.5 + - - +
9391 ARG* 2.8 26.2 + - - +
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Residues in contact with VAL 936 (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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9321 ILE 2.8 12.1 + - - -
9331 CYS* 3.5 6.3 - - - +
9351 THR* 1.3 73.1 - - - +
9371 LEU* 1.3 61.4 + - - +
9391 ARG* 4.3 0.2 - - - -
9401 LEU* 2.9 19.9 + - - -
9511 ALA* 5.4 12.3 - - - +
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Residues in contact with LEU 937 (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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9331 CYS 2.9 14.7 + - - -
9341 GLY 3.7 1.8 - - - -
9361 VAL* 1.3 74.2 - - - +
9381 TRP* 1.3 57.9 + - - +
9401 LEU* 2.4 30.1 + - - +
9411 ASN 3.0 5.2 + - - -
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Residues in contact with TRP 938 (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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9341 GLY 2.9 14.8 + - - -
9351 THR* 3.6 2.0 - - - +
9371 LEU* 1.3 75.0 - - - +
9391 ARG* 1.3 65.7 + - - +
9411 ASN* 3.2 6.9 + - - -
9421 ASN 3.8 6.8 + - - -
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Residues in contact with ARG 939 (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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9351 THR* 2.8 15.0 + - - +
9381 TRP* 1.3 70.9 - - - +
9401 LEU* 1.3 67.7 + - - +
9411 ASN 2.8 1.4 + - - -
9421 ASN 3.2 17.0 - - - +
9471 VAL 5.8 1.5 - - - -
9481 ARG* 5.4 3.1 - - - -
9511 ALA* 6.4 0.4 - - - -
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Residues in contact with LEU 940 (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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9361 VAL 2.9 15.0 + - - -
9371 LEU* 2.4 16.9 + - - +
9391 ARG* 1.3 70.7 - - - +
9411 ASN* 1.3 65.6 + - - +
9481 ARG* 4.3 19.4 - - - +
9511 ALA* 5.8 5.5 - - - +
9521 ALA 6.1 1.1 - - - +
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Residues in contact with ASN 941 (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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9371 LEU 3.0 9.5 + - - -
9381 TRP 3.2 2.8 + - - -
9391 ARG 2.8 1.6 + - - -
9401 LEU* 1.3 80.9 - - - +
9421 ASN* 1.3 67.9 + - - +
9441 SER* 5.1 0.2 - - - -
9451 ALA* 4.4 10.2 + - - -
9481 ARG* 5.4 0.2 - - - -
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Residues in contact with ASN 942 (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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9381 TRP 3.8 6.0 + - - -
9391 ARG* 3.2 13.8 + - - +
9401 LEU 4.2 0.2 - - - +
9411 ASN* 1.3 81.1 - - - +
9431 LYS* 1.3 64.4 + - - +
9441 SER* 2.9 8.7 + - - +
9451 ALA 4.3 1.7 + - - -
9471 VAL* 6.0 0.7 - - - -
9481 ARG 5.6 2.1 + - - -
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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