Contacts of the strand formed by residues 1271 - 1275 (chain A) 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 THR1271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1264A GLY* 3.8 30.5 - - - -
1265A ARG 3.5 5.6 - - - +
1266A ALA* 4.8 4.0 - - + +
1270A GLY* 1.3 72.7 - - - -
1272A MSE 1.3 61.9 + - - +
1273A MSE 4.0 4.1 + - - +
2235B ILE 4.0 0.2 - - - +
2236B LEU* 3.2 4.9 - - - +
2237B LEU* 3.2 27.3 + - + +
2238B GLU* 3.0 26.1 + - - -
4244D MSE 3.1 25.5 - - + +
4248D ARG* 3.8 8.8 + - - -
4256D ILE* 4.1 9.4 - - + -
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Residues in contact with MSE1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264A GLY* 3.3 1.8 - - - -
1265A ARG* 2.7 77.9 + - + +
1267A LEU* 3.9 28.2 - - + +
1270A GLY 3.9 0.8 + - - -
1271A THR* 1.3 75.3 - - - +
1273A MSE 1.3 62.7 + - - +
1274A VAL* 3.6 8.4 + - + -
2235B ILE* 3.7 24.2 - - + -
2236B LEU* 3.7 16.7 - - + +
2277B ASN* 4.4 18.6 - - - +
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Residues in contact with MSE1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262A ALA* 3.4 35.9 - - + +
1263A ARG 3.5 8.3 - - - -
1264A GLY* 4.0 13.9 - - - +
1271A THR* 4.8 7.2 - - - +
1272A MSE 1.3 77.2 - - - +
1274A VAL* 1.3 61.1 + - - +
2235B ILE* 3.7 11.0 + - - +
2237B LEU* 5.2 10.8 - - + +
2240B LYS* 4.3 20.6 - - - +
2277B ASN* 3.2 25.6 + - - +
2278B PRO* 3.5 24.6 - - + +
4256D ILE* 4.2 24.0 - - + +
4258D GLU* 3.9 26.0 - - + +
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Residues in contact with VAL1274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261A ILE 3.9 0.5 - - - +
1262A ALA* 3.3 3.3 - - - -
1263A ARG* 2.8 40.1 + - + +
1264A GLY 5.2 0.2 - - - -
1265A ARG* 3.8 56.8 - - + +
1272A MSE 3.9 9.2 - - + +
1273A MSE 1.3 77.2 - - - +
1275A SER* 1.3 71.5 + - - +
1276A ARG* 4.9 14.6 + - - +
2277B ASN* 3.3 15.3 - - - +
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Residues in contact with SER1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261A ILE 3.5 6.9 + - - -
1262A ALA* 4.3 1.7 - - - +
1273A MSE 4.1 0.4 - - - -
1274A VAL* 1.3 82.7 - - - +
1276A ARG* 1.3 69.1 + - - +
1277A ASN* 5.5 0.5 - - - +
2260B ASN* 4.2 5.5 + - - -
2275B SER* 3.6 18.2 - - - +
2276B ARG 2.9 28.3 + - - -
2277B ASN* 2.8 13.0 + - - +
2278B PRO* 3.3 19.2 - - - +
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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