Contacts of the helix formed by residues 1248 - 1262 (chain I) in PDB entry 5TJ4
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 ASN1248 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247I ARG* 1.3 80.3 - - - +
1249I MET* 1.3 61.9 + - - +
1250I LYS* 2.4 41.1 + - - +
1251I GLU* 3.4 17.5 - - + +
1252I LYS* 3.0 25.1 + - - +
1371I ASP* 3.4 19.0 + - - +
1373I LEU* 3.9 28.7 - - + +
1374I ALA* 5.4 1.6 - - - -
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Residues in contact with MET1249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247I ARG 3.9 1.2 + - - -
1248I ASN* 1.3 73.3 + - - +
1250I LYS* 1.3 65.7 + - - +
1251I GLU 3.2 1.6 - - - -
1252I LYS* 3.3 7.6 + - + +
1253I LEU* 3.1 31.1 + - + +
1256I MET* 5.4 0.3 - - - +
1366I MET* 3.6 22.2 - - + -
1371I ASP* 4.3 16.8 - - - +
1373I LEU 4.4 6.0 + - - +
1374I ALA* 5.5 2.3 - - + +
1390I CYS* 4.1 33.0 - - + +
1393I TYR* 3.5 34.1 - - + -
1394I VAL* 4.2 15.2 - - + +
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Residues in contact with LYS1250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248I ASN* 2.4 27.5 + - - +
1249I MET* 1.3 75.4 - - - +
1251I GLU* 1.3 59.3 + - - +
1253I LEU* 3.2 19.7 - - + +
1254I GLU* 3.2 21.7 + - - +
1371I ASP* 4.0 13.6 + - + +
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Residues in contact with GLU1251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247I ARG* 4.8 8.3 - - + -
1248I ASN* 3.2 27.4 + - + +
1249I MET 3.2 0.4 - - - -
1250I LYS* 1.3 76.3 - - - +
1252I LYS* 1.3 66.6 + - - +
1254I GLU* 3.0 10.9 + - - +
1255I ASP* 2.9 22.8 + - - +
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Residues in contact with LYS1252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247I ARG* 5.7 2.6 - - + +
1248I ASN 3.0 14.9 + - - +
1249I MET* 3.3 13.2 + - + +
1251I GLU* 1.3 75.4 - - - +
1253I LEU* 1.3 58.6 - - - +
1255I ASP* 3.3 6.8 + - - +
1256I MET* 3.0 43.3 + - + +
1331I ASP* 5.5 4.9 - - - +
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Residues in contact with LEU1253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249I MET* 3.1 18.3 + - + +
1250I LYS* 3.2 28.5 - - + +
1252I LYS* 1.3 72.9 - - - +
1254I GLU* 1.3 67.7 + - + +
1256I MET* 3.2 21.0 + - + +
1257I GLU* 2.8 46.4 + - + +
1393I TYR* 3.9 30.7 - - + +
1394I VAL* 5.0 8.3 - - + -
1397I SER* 5.6 10.1 - - - +
1398I ILE* 5.0 2.9 - - + +
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Residues in contact with GLU1254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250I LYS 3.2 10.3 + - - +
1251I GLU* 3.0 13.6 + - - +
1253I LEU* 1.3 86.7 - - + +
1255I ASP* 1.3 56.7 + - - +
1257I GLU* 4.0 6.6 - - - +
1258I SER* 3.1 28.2 + - - -
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Residues in contact with ASP1255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251I GLU 2.9 12.1 + - - +
1252I LYS* 3.4 11.0 - - - +
1254I GLU* 1.3 73.5 - - - +
1256I MET* 1.3 67.5 + - + +
1258I SER* 3.2 7.8 + - - -
1259I VAL* 3.1 29.5 + - + +
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Residues in contact with MET1256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252I LYS* 3.0 16.8 + - + +
1253I LEU* 3.2 36.3 - - + +
1255I ASP* 1.3 78.0 - - + +
1257I GLU* 1.3 62.9 + - - +
1259I VAL* 3.3 4.7 + - - +
1260I LEU* 3.2 29.8 + - + +
1328I ALA* 4.2 27.1 - - + +
1331I ASP* 3.5 38.6 - - - +
1332I PHE* 4.5 4.7 - - - -
1394I VAL* 3.7 32.3 - - + -
1398I ILE* 3.8 18.4 - - + -
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Residues in contact with GLU1257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253I LEU* 2.8 26.7 + - + +
1254I GLU* 4.1 10.1 - - - +
1256I MET* 1.3 72.6 - - - +
1258I SER* 1.3 59.7 + - - +
1260I LEU* 3.5 5.1 + - - +
1261I LYS* 2.9 32.2 + - + +
1397I SER 6.1 0.7 - - - +
1398I ILE* 4.4 12.1 - - + +
1401I GLU* 5.0 16.0 - - + +
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Residues in contact with SER1258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254I GLU 3.1 20.3 + - - -
1255I ASP* 3.2 8.5 + - - -
1257I GLU* 1.3 75.6 - - - +
1259I VAL* 1.3 65.3 + - - +
1261I LYS* 3.6 12.9 + - - +
1262I ASP* 3.6 13.5 + - - +
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Residues in contact with VAL1259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255I ASP* 3.1 17.5 + - + +
1256I MET* 3.7 7.6 - - - +
1258I SER* 1.3 75.9 - - - +
1260I LEU* 1.3 66.8 + - + +
1262I ASP* 3.5 22.6 + - - +
1263I LEU* 4.1 3.3 - - - +
1322I VAL* 5.4 1.8 - - + -
1324I ALA* 3.9 27.6 - - + +
1325I ARG* 3.4 45.2 + - + +
1328I ALA* 4.6 4.3 - - + -
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Residues in contact with LEU1260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256I MET 3.2 17.2 + - - +
1257I GLU* 4.1 4.5 - - - +
1259I VAL* 1.3 83.1 - - + +
1261I LYS* 1.3 66.1 + - - +
1263I LEU* 3.5 33.9 - - + +
1268I ARG* 5.5 2.1 - - - +
1271I VAL* 5.5 3.1 - - + -
1325I ARG* 5.3 4.7 - - + +
1328I ALA* 4.5 15.0 - - + -
1329I ILE* 4.5 19.1 - - + -
1398I ILE* 3.7 36.3 - - + +
1401I GLU* 5.7 6.5 - - + -
1402I LEU* 4.0 30.6 - - + +
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Residues in contact with LYS1261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257I GLU* 2.9 20.5 + - + +
1258I SER* 3.6 9.6 - - - +
1259I VAL 3.3 0.2 - - - -
1260I LEU* 1.3 77.6 - - - +
1262I ASP* 1.3 57.0 + - - +
1263I LEU 2.9 12.3 + - - +
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Residues in contact with ASP1262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258I SER 3.6 7.1 + - - +
1259I VAL* 3.5 12.8 + - - +
1260I LEU 3.3 0.6 - - - -
1261I LYS* 1.3 73.4 - - - +
1263I LEU* 1.3 65.7 + - - +
1325I ARG* 4.0 12.6 + - - -
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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