Contacts of the strand formed by residues 4271 - 4275 (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 THR4271 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244A MSE 3.0 29.1 - - + +
1248A ARG* 3.8 8.7 + - - -
1256A ILE* 4.1 8.3 - - + -
3236C LEU* 3.6 2.5 - - - -
3237C LEU* 2.9 32.7 + - + +
3238C GLU* 2.8 23.7 + - - -
4264D GLY* 3.8 28.5 - - - -
4265D ARG 3.4 9.6 - - - +
4266D ALA* 4.7 4.8 - - + +
4270D GLY* 1.3 71.9 - - - -
4272D MSE 1.3 62.8 + - - +
4273D MSE 4.0 3.4 + - - +
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Residues in contact with MSE4272 (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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3235C ILE* 3.9 23.8 - - + +
3236C LEU* 3.5 20.4 - - + -
3277C ASN* 4.7 14.1 - - - +
4264D GLY* 3.3 1.7 - - - -
4265D ARG* 2.7 75.1 + - + +
4267D LEU* 3.9 26.2 - - + +
4270D GLY 3.9 1.6 + - - -
4271D THR* 1.3 75.7 - - - +
4273D MSE 1.3 62.9 + - - +
4274D VAL* 3.5 13.9 + - + -
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Residues in contact with MSE4273 (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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1256A ILE* 4.3 21.5 - - + +
1258A GLU* 3.7 30.7 - - + +
3235C ILE* 4.0 10.0 + - - +
3237C LEU* 5.1 12.6 - - + -
3240C LYS* 4.1 21.1 - - - +
3277C ASN* 3.8 10.2 + - - +
3278C PRO* 3.6 28.4 - - + +
4262D ALA* 3.4 41.7 - - + +
4263D ARG* 3.6 7.6 - - - -
4264D GLY* 3.9 13.9 - - - +
4271D THR* 4.9 5.8 - - - +
4272D MSE 1.3 76.7 - - - +
4274D VAL* 1.3 60.7 + - - +
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Residues in contact with VAL4274 (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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3277C ASN* 3.8 11.7 - - - +
4261D ILE 4.0 0.3 - - - +
4262D ALA* 3.1 3.5 - - - -
4263D ARG* 2.8 39.4 + - + +
4265D ARG* 3.8 57.9 - - + +
4272D MSE 4.0 11.4 - - + +
4273D MSE 1.3 77.2 - - - +
4275D SER* 1.3 71.3 + - - +
4276D ARG* 5.0 15.6 + - - +
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Residues in contact with SER4275 (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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3260C ASN* 4.1 6.1 + - - -
3275C SER* 4.0 11.8 - - - -
3276C ARG 3.2 25.4 + - - -
3277C ASN* 3.1 13.2 + - - +
3278C PRO* 3.2 20.6 - - - +
4261D ILE 3.6 6.4 + - - -
4262D ALA* 4.3 2.5 - - - +
4273D MSE 4.0 0.6 + - - -
4274D VAL* 1.3 83.1 - - - +
4276D ARG* 1.3 71.2 + - - +
4277D ASN* 4.4 0.7 + - - +
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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