Contacts of the strand formed by residues 4184 - 4188 (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 VAL4184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4148D THR* 4.0 17.7 - - + -
4152D ALA* 3.9 20.2 - - + -
4157D ARG* 4.2 3.5 + - - -
4158D VAL* 3.4 15.3 - - + +
4160D ALA* 4.4 4.3 - - + -
4175D LEU* 4.1 9.0 - - + -
4181D GLY* 3.4 28.5 - - - +
4182D ASP 3.1 4.7 - - - +
4183D ASN* 1.3 95.3 - - - +
4185D THR* 1.3 63.7 + - - +
4186D LEU* 3.7 31.2 + - + +
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Residues in contact with THR4185 (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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4157D ARG* 2.7 34.2 + - - +
4158D VAL 2.9 8.8 + - - -
4159D TYR* 3.7 28.0 - - + -
4160D ALA 3.0 25.1 + - - +
4184D VAL* 1.3 71.4 - - - +
4186D LEU* 1.3 62.9 + - - +
4187D MSE 3.7 22.9 + - + +
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Residues in contact with LEU4186 (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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4160D ALA* 3.7 16.6 - - + -
4168D ILE* 3.8 30.5 - - + +
4171D THR* 4.2 16.8 - - + -
4172D GLU* 3.6 47.3 - - + +
4175D LEU* 4.2 3.1 - - + -
4184D VAL* 3.7 26.7 + - + +
4185D THR* 1.3 74.6 - - - +
4187D MSE 1.3 62.5 + - - +
4188D GLU 4.2 1.2 + - - -
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Residues in contact with MSE4187 (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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4159D TYR* 3.5 21.5 - - + -
4160D ALA 2.9 8.2 + - - +
4161D ILE* 3.2 47.3 - - + +
4162D ASP 3.5 2.3 + - - -
4168D ILE* 3.5 11.8 - - - +
4185D THR* 3.8 20.9 - - + +
4186D LEU* 1.3 79.6 - - - +
4188D GLU* 1.3 63.9 + - - +
4189D GLY 3.8 0.2 + - - -
4194D ALA* 4.1 21.7 - - + +
4197D LYS* 5.7 5.4 - - - -
4198D ILE* 3.1 42.6 - - + -
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Residues in contact with GLU4188 (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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4162D ASP 3.6 7.6 - - - +
4163D ARG 4.1 4.5 - - - +
4165D PRO* 3.4 37.9 - - + +
4168D ILE* 3.8 27.3 - - + +
4186D LEU 4.2 1.4 + - - -
4187D MSE 1.3 74.9 - - - +
4189D GLY* 1.3 62.8 + - - +
4194D ALA* 5.7 2.6 - - - +
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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