Contacts of the helix formed by residues 1542 - 1554 (chain D) 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 MET1542 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1538D ARG 3.0 12.2 + - - -
1539D LEU 3.5 5.6 + - - -
1540D LEU 3.1 0.8 - - - -
1541D SER* 1.3 79.5 - - - +
1543D ALA* 1.3 64.2 + - - +
1544D LYS 3.6 0.4 - - - -
1545D PRO* 3.6 6.0 - - - +
1546D VAL* 3.3 15.4 + - - -
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Residues in contact with ALA1543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539D LEU 3.8 4.2 + - - -
1540D LEU 3.1 15.7 + - - -
1541D SER 3.3 0.6 - - - -
1542D MET* 1.3 77.1 - - - +
1544D LYS* 1.3 62.1 + - - +
1546D VAL* 3.1 12.5 + - - -
1547D TYR* 3.6 6.6 + - - -
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Residues in contact with LYS1544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540D LEU 4.8 0.8 + - - -
1541D SER 4.8 2.4 + - - -
1543D ALA* 1.3 73.5 - - - +
1545D PRO* 1.4 63.3 - - - +
1546D VAL 3.1 1.0 + - - -
1547D TYR* 3.1 5.0 + - - +
1548D HIS* 3.1 17.2 + - - -
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Residues in contact with PRO1545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1541D SER 5.0 2.4 - - - -
1542D MET* 3.6 10.5 - - - +
1543D ALA 3.3 0.8 - - - -
1544D LYS* 1.4 73.4 - - - +
1546D VAL* 1.3 52.1 + - - +
1548D HIS* 3.6 3.1 - - - +
1549D ALA* 2.7 31.9 + - - -
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Residues in contact with VAL1546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542D MET 3.3 9.3 + - - -
1543D ALA 3.1 10.5 + - - -
1545D PRO* 1.3 75.2 - - - +
1547D TYR* 1.3 63.8 + - - +
1549D ALA* 3.0 3.5 + - - +
1550D ILE* 3.0 18.2 + - - -
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Residues in contact with TYR1547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543D ALA 3.6 5.7 + - - -
1544D LYS* 3.1 7.1 + - - +
1546D VAL* 1.3 73.0 - - - +
1548D HIS* 1.3 62.5 + - - +
1550D ILE* 3.0 5.0 + - - +
1551D THR* 3.0 19.8 + - - -
1576D ILE* 6.1 4.9 - - - +
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Residues in contact with HIS1548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1544D LYS 3.1 12.9 + - - -
1545D PRO* 3.6 4.0 - - - -
1547D TYR* 1.3 74.3 - - - +
1549D ALA* 1.3 57.7 + - - +
1551D THR* 3.3 2.3 + - - +
1552D LYS* 2.9 27.7 + - - -
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Residues in contact with ALA1549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1545D PRO 2.7 18.5 + - - -
1546D VAL* 3.0 5.3 + - - +
1548D HIS* 1.3 72.2 - - - +
1550D ILE* 1.3 57.1 + - - +
1552D LYS* 5.2 0.4 - - - +
1553D HIS* 3.0 27.0 + - - +
1554D SER 4.0 0.7 + - - -
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Residues in contact with ILE1550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546D VAL 3.0 8.3 + - - -
1547D TYR* 3.0 7.5 + - - +
1549D ALA* 1.3 72.8 - - - +
1551D THR* 1.3 62.1 + - - +
1552D LYS 3.0 4.0 - - - -
1554D SER* 2.9 39.4 + - - +
1555D PRO* 4.4 1.1 - - - -
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Residues in contact with THR1551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547D TYR 3.0 12.5 + - - -
1548D HIS* 3.3 4.0 + - - +
1550D ILE* 1.3 73.5 - - - +
1552D LYS* 1.3 60.3 + - - +
1555D PRO* 4.4 13.5 - - - +
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Residues in contact with LYS1552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548D HIS 2.9 14.9 + - - -
1549D ALA* 4.1 0.4 - - - +
1550D ILE 3.0 0.4 + - - -
1551D THR* 1.3 81.6 - - - +
1553D HIS* 1.3 63.3 + - - +
1554D SER 3.6 0.2 + - - -
1555D PRO 4.5 2.4 - - - -
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Residues in contact with HIS1553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549D ALA 3.0 15.8 + - - -
1552D LYS* 1.3 74.7 - - - +
1554D SER* 1.3 56.7 + - - +
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Residues in contact with SER1554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549D ALA 4.0 2.4 + - - -
1550D ILE* 2.9 17.0 + - - +
1553D HIS* 1.3 79.1 - - - +
1555D PRO* 1.3 66.9 - - - +
1556D LYS 3.4 2.4 + - - -
1557D LYS* 3.7 20.9 - - - +
1660D LEU* 5.9 7.6 - - - +
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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