Contacts of the strand formed by residues 4279 - 4284 (chain D) in PDB entry 1F38
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 VAL4279 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4117D THR* 5.3 5.6 - - + -
4118D ALA* 5.8 3.8 - - + +
4121D VAL* 3.9 41.1 - - + -
4233D THR* 4.5 11.0 - - + -
4234D ALA 3.7 8.3 - - - +
4235D ILE* 3.9 17.5 - - + -
4257D THR 3.9 0.7 - - - +
4258D GLU* 3.4 4.2 - - - -
4259D LEU* 2.8 34.4 + - - +
4261D ILE* 6.0 1.8 - - + -
4276D ARG* 6.2 0.7 - - + -
4277D ASN 3.5 11.4 - - - +
4278D PRO* 1.3 79.0 - - - +
4280D ALA* 1.3 72.3 + - - +
4281D LEU* 4.5 2.5 - - + +
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Residues in contact with ALA4280 (chain D).
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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4233D THR* 3.6 0.3 - - - -
4234D ALA* 2.9 34.9 + - + +
4240D LYS* 3.7 36.9 - - + +
4256D ILE* 4.0 11.7 - - + -
4257D THR 3.4 5.4 - - - +
4258D GLU* 3.9 13.9 - - + +
4279D VAL* 1.3 76.0 - - - +
4281D LEU* 1.3 71.0 + - - +
4282D ILE* 4.1 2.0 - - + -
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Residues in contact with LEU4281 (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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4121D VAL* 4.0 22.7 - - + +
4124D LEU* 3.7 37.5 - - + -
4125D ILE* 4.2 19.5 - - + -
4128D LEU* 4.0 17.7 - - + -
4231D ILE* 4.5 10.3 - - + -
4232D VAL 3.3 5.4 - - - +
4233D THR* 3.8 20.0 - - - +
4256D ILE* 3.3 3.6 - - - -
4257D THR* 3.0 35.6 + - - +
4259D LEU* 5.5 3.4 - - + -
4279D VAL* 4.5 4.0 - - + +
4280D ALA* 1.3 82.9 - - - +
4282D ILE* 1.3 64.6 + - - +
4283D TYR* 3.6 4.6 - - + -
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Residues in contact with ILE4282 (chain D).
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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4230D ILE 4.0 0.3 - - - +
4231D ILE* 3.5 1.2 - - - -
4232D VAL* 2.7 45.3 + - + +
4234D ALA* 3.9 25.4 - - + -
4240D LYS* 4.2 11.4 - - - +
4243D ALA* 3.8 24.9 - - + -
4244D MSE 4.0 19.7 - - + +
4247D LEU* 3.7 17.9 - - + +
4254D VAL* 3.4 30.7 - - + -
4255D ASN 3.3 4.9 - - - +
4256D ILE* 4.1 9.6 - - + -
4280D ALA* 4.2 9.2 - - + -
4281D LEU* 1.3 76.6 - - - +
4283D TYR* 1.3 57.7 + - - +
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Residues in contact with TYR4283 (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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4128D LEU* 3.9 41.5 - - + +
4230D ILE 3.3 11.2 - - - +
4231D ILE* 4.0 15.7 - - + -
4247D LEU* 5.2 0.4 - - - -
4254D VAL* 3.8 3.3 - - - -
4255D ASN* 2.9 74.9 + - + +
4256D ILE 5.3 0.2 - - - -
4257D THR* 3.8 25.1 + - - -
4281D LEU* 3.6 11.7 - - + -
4282D ILE* 1.3 75.9 - - - +
4284D THR* 1.3 73.0 + - - +
4285D GLY* 6.0 0.7 - - - -
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Residues in contact with THR4284 (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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4228D GLY 4.4 2.1 + - - -
4229D ARG* 4.1 6.2 - - - +
4230D ILE* 3.1 36.5 + - + +
4247D LEU* 4.1 22.0 - - + -
4252D PHE* 3.5 47.6 - - + -
4253D ASP 3.5 4.9 - - - +
4254D VAL* 4.8 0.7 - - - +
4283D TYR* 1.3 87.7 - - - +
4285D GLY* 1.3 74.6 + - - +
4286D VAL* 3.6 5.2 + - - +
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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