Contacts of the strand formed by residues 1767 - 1772 (chain X) in PDB entry 3HM6
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 VAL1767 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752X ASN* 4.5 0.4 - - - -
1753X ALA* 2.5 52.4 + - + +
1765X GLN 3.9 3.6 + - - -
1766X GLY* 1.3 72.5 - - - -
1768X PRO* 1.4 65.9 - - + +
1787X GLN* 4.9 18.4 - - + +
1788X LEU* 5.3 5.8 - - + -
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Residues in contact with PRO1768 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750X THR* 4.4 12.3 - - + -
1751X LEU 3.2 10.8 - - - +
1752X ASN* 4.5 2.2 - - - -
1766X GLY 4.4 2.0 - - - +
1767X VAL* 1.4 85.4 - - + +
1769X VAL* 1.3 68.2 + - - +
1770X LYS 4.4 0.4 + - - -
1787X GLN* 3.9 15.9 - - - +
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Residues in contact with VAL1769 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750X THR* 3.2 5.5 - - - +
1751X LEU* 2.8 41.2 + - + +
1753X ALA* 3.4 28.0 - - + -
1767X VAL* 4.9 0.7 - - + -
1768X PRO* 1.3 81.0 - - - +
1770X LYS* 1.3 62.6 + - - +
1771X VAL* 3.2 31.6 + - + +
1783X LYS* 3.5 26.5 - - + +
1784X MET* 4.0 18.4 - - + +
1787X GLN* 3.9 17.5 - - + +
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Residues in contact with LYS1770 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719X ASP* 5.2 4.3 - - - +
1749X LEU 3.7 6.5 - - - +
1750X THR* 4.2 11.3 - - + +
1768X PRO 4.4 0.2 - - - -
1769X VAL* 1.3 72.1 - - - +
1771X VAL* 1.3 63.2 + - - +
1783X LYS* 4.0 13.7 + - - +
1787X GLN* 5.3 3.0 + - - -
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Residues in contact with VAL1771 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719X ASP 5.6 0.2 - - - -
1748X PRO* 4.1 0.9 - - - +
1749X LEU* 2.7 46.8 + - + +
1751X LEU* 3.5 36.1 - - + -
1769X VAL* 3.2 26.0 + - + -
1770X LYS* 1.3 74.9 - - - +
1772X LEU* 1.3 70.0 + - - +
1775X ASP* 4.3 3.4 - - - +
1780X ALA* 4.4 13.2 - - + +
1783X LYS* 4.0 20.2 - - + -
1784X MET* 4.9 0.2 - - + -
1836X LEU* 3.7 20.0 - - + -
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Residues in contact with LEU1772 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719X ASP 3.6 16.6 - - - +
1720X LYS* 3.7 15.5 - - - +
1721X GLY* 3.1 39.7 - - - +
1722X PRO 3.9 2.0 - - - -
1746X TYR* 3.8 14.6 - - + -
1747X ARG 3.7 4.5 - - - +
1748X PRO* 3.7 22.0 - - + -
1749X LEU* 4.0 5.6 - - - +
1771X VAL* 1.3 82.6 - - - +
1773X ASP* 1.3 64.8 + - - +
1774X CYS* 3.3 13.5 - - - -
1775X ASP* 3.2 32.3 + - - +
1783X LYS* 3.9 6.5 - - - +
1836X LEU* 3.4 10.4 - - - +
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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