Contacts of the helix formed by residues 1239 - 1252 (chain A) in PDB entry 4UP5
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 THR1239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A TRP* 3.9 2.5 - - - -
378A ALA* 3.6 21.1 - - + +
379A CYS 5.5 2.5 - - - +
380A ASP* 5.3 7.0 - - - +
382A CYS 5.9 1.8 - - - +
1237A VAL* 5.7 1.8 - - + -
1238A PHE* 1.3 74.9 - - - +
1240A THR* 1.3 61.3 + - - +
1241A HIS* 3.7 5.5 + - - +
1242A LEU* 3.1 28.3 + - + +
1243A ALA* 2.9 28.1 + - - +
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Residues in contact with THR1240 (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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359A THR* 3.4 13.0 - - - +
360A GLY 3.7 3.8 - - - -
361A MET* 3.4 43.1 - - + +
377A TRP* 3.0 23.8 + - - +
378A ALA 4.2 1.2 + - - -
380A ASP* 4.9 5.8 + - - -
1239A THR* 1.3 76.1 - - - +
1241A HIS* 1.3 68.2 + - + +
1243A ALA* 3.2 1.2 + - - +
1244A ASN* 2.8 34.7 + - - +
1385A 94W 3.2 23.6 + - - -
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Residues in contact with HIS1241 (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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359A THR 5.4 3.0 + - - -
360A GLY* 6.1 1.0 - - - -
380A ASP* 5.7 7.9 + - - -
1239A THR* 3.3 5.4 + - - +
1240A THR* 1.3 90.4 - - + +
1242A LEU* 1.3 58.4 + - - +
1244A ASN* 3.3 11.6 + - - +
1245A THR* 2.9 34.6 + - - +
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Residues in contact with LEU1242 (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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1237A VAL 4.1 18.8 - - - +
1238A PHE* 4.0 14.4 - - + -
1239A THR* 3.1 25.2 + - + +
1241A HIS* 1.3 74.6 - - - +
1243A ALA* 1.3 59.9 + - - +
1245A THR* 3.3 7.3 + - + -
1246A ALA* 2.8 31.5 + - - +
1261A TYR* 3.8 36.6 - - + +
1262A HIS 4.4 9.9 - - - +
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Residues in contact with ALA1243 (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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361A MET* 4.6 2.7 - - + -
365A ALA* 3.6 14.1 - - + +
369A LEU* 4.0 29.2 - - + -
1238A PHE* 4.0 15.8 - - + -
1239A THR 2.9 21.6 + - - +
1240A THR* 3.7 5.4 - - - +
1242A LEU* 1.3 73.1 - - - +
1244A ASN* 1.3 58.5 + - - +
1246A ALA* 3.4 2.4 + - - +
1247A ALA* 2.9 32.7 + - - +
1258A ILE* 4.9 4.0 - - + +
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Residues in contact with ASN1244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY 3.1 25.9 + - - -
361A MET* 3.4 7.5 - - - +
362A THR* 2.9 41.9 + - + +
365A ALA* 3.4 8.4 - - - +
1240A THR* 2.8 23.3 + - - +
1241A HIS* 3.6 11.7 - - - +
1243A ALA* 1.3 78.7 - - - +
1245A THR* 1.3 62.5 + - - +
1247A ALA* 3.5 2.1 + - - +
1248A GLU* 3.2 23.2 + - - +
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Residues in contact with THR1245 (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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1241A HIS* 2.9 18.1 + - - +
1242A LEU* 3.7 8.7 - - + -
1244A ASN* 1.3 74.8 - - - +
1246A ALA* 1.4 63.8 + - - +
1248A GLU* 3.3 7.8 + - - +
1249A ALA* 3.1 21.3 + - - +
1254A ARG* 5.1 2.7 + - - +
1261A TYR* 3.8 23.6 - - + +
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Residues in contact with ALA1246 (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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1238A PHE* 4.3 5.4 - - + -
1242A LEU 2.8 21.0 + - - +
1243A ALA 3.8 2.2 - - - +
1245A THR* 1.4 73.4 - - - +
1247A ALA* 1.3 57.6 + - - +
1249A ALA* 3.2 4.0 + - - +
1250A VAL* 2.9 32.2 + - - +
1258A ILE* 3.8 24.7 - - + +
1261A TYR* 3.5 37.5 - - + -
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Residues in contact with ALA1247 (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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362A THR* 4.9 0.4 - - - +
364A SER* 4.1 7.6 - - - -
365A ALA* 3.6 30.5 - - + +
368A LEU* 3.7 23.8 - - + -
1243A ALA 2.9 21.4 + - - +
1244A ASN 4.0 2.9 - - - +
1246A ALA* 1.3 73.2 - - - +
1248A GLU* 1.3 57.7 + - - +
1250A VAL* 3.3 1.6 + - - +
1251A LEU* 2.9 36.4 + - - +
1258A ILE* 3.8 3.7 - - + +
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Residues in contact with GLU1248 (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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364A SER* 5.9 0.4 - - - -
1244A ASN 3.2 17.4 + - - +
1245A THR* 3.7 7.8 - - - +
1247A ALA* 1.3 73.4 - - - +
1249A ALA* 1.3 59.5 + - - +
1251A LEU* 3.2 6.9 + - - +
1252A GLN* 2.9 61.7 + - + +
1254A ARG* 4.8 4.1 + - - +
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Residues in contact with ALA1249 (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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1245A THR 3.1 9.5 + - - +
1246A ALA 3.4 9.0 - - - +
1248A GLU* 1.3 76.5 - - - +
1250A VAL* 1.3 58.9 + - - +
1252A GLN* 3.4 1.4 + - - -
1253A GLY 3.3 3.5 + - - -
1254A ARG* 2.9 53.2 + - + +
1255A ALA* 4.0 7.0 - - + -
1261A TYR* 3.4 39.3 - - + +
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Residues in contact with VAL1250 (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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368A LEU* 4.2 21.1 - - + -
1246A ALA 2.9 21.2 + - - +
1247A ALA 3.3 6.9 + - - +
1249A ALA* 1.3 69.4 - - - +
1251A LEU* 1.3 65.6 + - + +
1253A GLY* 3.0 19.6 + - - -
1255A ALA* 3.7 20.5 - - + +
1256A ASP 5.0 2.5 - - - +
1257A SER* 3.5 39.5 - - - +
1258A ILE* 3.6 10.1 - - + +
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Residues in contact with LEU1251 (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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364A SER* 3.9 30.3 - - - +
368A LEU* 4.7 14.4 - - + -
1247A ALA 2.9 20.8 + - - +
1248A GLU* 3.9 4.9 - - - +
1250A VAL* 1.3 86.1 - - + +
1252A GLN* 1.3 60.3 + - + +
1253A GLY 3.1 1.3 - - - -
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Residues in contact with GLN1252 (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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1248A GLU* 2.9 45.0 + - + +
1249A ALA 3.8 3.8 - - - +
1250A VAL 3.3 0.4 - - - -
1251A LEU* 1.3 76.7 - - + +
1253A GLY* 1.3 60.2 + - - +
1254A ARG* 2.5 54.1 + - + +
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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