Contacts of the strand formed by residues 4201 - 4206 (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 ILE4201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4136D VAL* 3.3 21.1 - - + +
4137D ALA 4.3 0.2 - - - -
4138D VAL* 3.6 39.7 - - + +
4195D LEU* 5.7 2.5 - - + -
4198D ILE* 4.3 8.1 - - + -
4199D PRO 4.2 7.4 - - - +
4200D ASP* 1.3 81.1 - - - +
4202D ASP* 1.3 61.4 + - - +
4203D ILE 4.1 5.8 - - - +
4204D ALA* 3.9 13.5 - - + -
4220D ILE* 4.1 17.5 - - + -
4223D LYS* 2.8 25.1 + - + +
4224D LEU* 3.5 13.0 - - + +
4225D LYS* 2.8 28.5 + - - -
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Residues in contact with ASP4202 (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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4134D ASN 4.2 2.3 - - - +
4135D ASP* 3.2 36.8 - - + +
4136D VAL* 2.7 27.5 + - - +
4201D ILE* 1.3 74.3 - - - +
4203D ILE* 1.3 62.7 + - - +
4224D LEU* 4.4 1.1 - - - -
4225D LYS* 3.1 40.6 + - - +
4226D PRO 5.1 3.1 - - - +
4227D GLY 6.1 0.2 - - - -
4228D GLY* 3.0 11.2 - - - -
4229D ARG* 2.8 35.5 + - - +
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Residues in contact with ILE4203 (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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4129D ALA* 3.8 35.7 - - + +
4131D PRO* 3.9 23.3 - - + -
4135D ASP* 4.0 15.0 - - + +
4136D VAL 3.4 2.7 + - - +
4137D ALA* 3.1 16.5 - - + -
4138D VAL* 3.1 24.9 + - - +
4151D LEU* 4.6 7.0 - - + -
4155D VAL* 4.2 9.2 - - + -
4201D ILE* 4.1 4.3 - - - +
4202D ASP* 1.3 88.9 - - + +
4204D ALA* 1.3 64.3 + - - +
4205D VAL* 4.2 15.5 - - + -
4224D LEU* 5.1 0.2 - - - -
4229D ARG* 3.5 24.9 - - + +
4231D ILE* 5.4 0.9 - - + -
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Residues in contact with ALA4204 (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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4138D VAL* 3.6 18.6 - - + -
4201D ILE* 3.9 5.6 - - + -
4203D ILE* 1.3 74.5 - - - +
4205D VAL* 1.3 62.8 + - - +
4220D ILE* 3.7 37.2 - - + -
4224D LEU* 4.8 0.9 - - + -
4229D ARG 2.8 14.4 + - - +
4230D ILE* 3.3 7.6 - - + +
4231D ILE* 2.9 26.0 + - - +
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Residues in contact with VAL4205 (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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4125D ILE* 4.1 31.9 - - + -
4129D ALA* 5.4 1.1 - - + -
4138D VAL 3.0 8.8 + - - +
4139D ASP* 3.5 19.2 - - - +
4140D VAL* 2.9 26.3 + - - +
4147D VAL* 4.1 22.9 - - + -
4151D LEU* 4.5 6.7 - - + -
4203D ILE* 4.2 16.4 - - + -
4204D ALA* 1.3 77.1 - - - +
4206D VAL* 1.3 68.2 + - - +
4207D GLY* 4.1 1.3 - - - +
4231D ILE* 3.3 16.2 - - + +
4233D THR* 4.9 5.4 - - - +
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Residues in contact with VAL4206 (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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4140D VAL* 3.7 16.6 - - + +
4205D VAL* 1.3 78.2 - - - +
4207D GLY* 1.3 68.6 + - - +
4209D SER* 4.3 11.2 - - - -
4213D LEU* 4.0 23.3 - - + -
4216D ILE* 4.2 7.6 - - + -
4217D LEU* 4.2 14.4 - - + -
4220D ILE* 3.6 29.6 - - + -
4230D ILE* 4.9 4.3 - - + -
4231D ILE 2.9 9.6 + - - +
4232D VAL* 3.4 13.9 - - + +
4233D THR* 2.8 28.3 + - - -
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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