Contacts of the strand formed by residues 1418 - 1420 (chain F) in PDB entry 1IV4
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 LEU1418 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412F LEU* 4.3 23.3 - - + -
1416F ARG 3.7 0.8 + - - -
1417F PRO* 1.3 72.9 - - - +
1419F TYR* 1.3 72.6 + - - +
1420F LEU* 4.2 25.6 - - + -
1424F LEU* 3.4 5.7 - - - +
1425F ILE* 2.8 51.2 + - + +
1427F SER* 3.8 7.7 - - - +
1429F VAL* 3.4 15.5 - - + +
1430F GLY* 4.0 2.2 - - - -
1431F ALA* 4.6 5.6 - - + +
1437F GLY 5.6 1.3 - - - +
1500F LEU* 4.3 6.7 - - + -
1502F ARG 5.1 0.2 - - - +
1503F PRO* 3.6 33.2 - - + -
1542F VAL* 5.1 8.5 - - + -
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Residues in contact with TYR1419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1417F PRO* 3.6 35.1 + - + +
1418F LEU* 1.3 77.8 - - - +
1420F LEU* 1.3 70.0 - - - +
1422F GLY 5.1 4.3 - - - -
1423F LEU* 3.3 4.9 - - - +
1424F LEU* 3.5 48.7 - - + +
1431F ALA* 5.5 0.6 - - - +
1436F ASP* 3.6 42.1 + - + +
1437F GLY 4.1 3.1 + - - +
1438F ASP* 3.3 32.1 + - + +
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Residues in contact with LEU1420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1418F LEU* 4.1 24.3 + - + -
1419F TYR* 1.3 81.4 - - - +
1421F CYS* 1.3 73.4 + - - +
1422F GLY 3.0 1.6 - - - -
1423F LEU 2.9 18.4 + - - +
1425F ILE* 4.2 9.4 - - + -
1437F GLY 5.7 0.2 - - - +
1438F ASP* 3.5 2.0 - - - -
1439F ALA 4.3 2.7 - - - +
1440F ALA* 4.1 21.8 - - + +
1498F LEU* 4.1 17.5 - - + -
1500F LEU* 4.6 7.6 - - + -
1505F LEU* 3.9 37.9 - - + -
1512F LEU* 3.2 17.8 - - + +
1542F VAL* 4.2 20.6 - - + -
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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
------------------------------------------------------------
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