Contacts of the helix formed by residues 1341 - 1353 (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 GLU1341 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179I LYS* 5.1 9.2 - - - +
1222I ALA* 4.0 18.4 - - + +
1225I ASP* 6.4 2.5 - - + -
1229I ARG* 5.7 1.3 - - - +
1340I SER* 1.3 87.3 + - - +
1342I GLU* 1.3 69.3 + - - +
1343I GLN 3.2 0.2 + - - -
1344I GLN* 3.1 37.4 + - - +
1345I PHE* 3.7 7.6 - - + -
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Residues in contact with GLU1342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I ALA* 3.3 24.6 - - - +
1222I ALA* 3.6 4.5 - - + -
1223I GLY* 3.2 25.5 - - - +
1229I ARG* 2.5 28.0 + - - -
1339I LEU* 4.0 20.6 - - + -
1340I SER 2.7 24.7 + - - -
1341I GLU* 1.3 77.2 + - - +
1343I GLN* 1.3 53.7 + - - +
1345I PHE* 2.7 36.9 + - - +
1346I VAL* 2.9 13.0 + - + +
1388I ILE* 3.6 7.3 - - - +
1392I LEU* 4.5 11.2 - - + -
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Residues in contact with GLN1343 (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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1278I CYS 3.4 9.7 - - - +
1279I LEU* 3.5 12.1 - - + +
1280I GLY* 2.7 39.6 + - - +
1281I LYS 5.5 0.3 - - - -
1282I GLU* 4.9 10.5 + - - +
1285I ARG* 5.6 1.3 - - - +
1336I LEU* 3.3 36.9 + - + +
1337I LEU 5.0 0.4 + - - -
1339I LEU* 2.8 33.9 + - + -
1340I SER* 3.5 14.2 + - - +
1341I GLU 3.2 0.4 - - - -
1342I GLU* 1.3 76.9 - - - +
1344I GLN* 1.3 64.9 + - - +
1346I VAL* 3.1 12.2 + - - +
1347I ALA* 2.9 23.1 + - - +
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Residues in contact with GLN1344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I LYS* 4.8 9.5 - - - +
1279I LEU 5.7 0.9 - - - -
1280I GLY* 5.1 8.3 - - - +
1340I SER 4.8 0.2 + - - -
1341I GLU* 3.1 32.9 + - - +
1343I GLN* 1.3 77.7 - - - +
1345I PHE* 1.3 87.0 + - + +
1347I ALA* 3.4 9.4 - - - +
1348I GLU* 3.1 26.3 + - - +
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Residues in contact with PHE1345 (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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179I LYS* 4.2 25.1 - - + -
365I GLN* 6.4 1.1 - - + -
366I THR* 3.3 16.8 - - + +
369I ALA* 3.5 33.4 - - + -
370I ALA* 3.6 36.8 - - + -
1222I ALA* 4.5 7.0 - - + -
1341I GLU* 3.7 22.4 - - + -
1342I GLU* 2.7 13.9 + - - +
1344I GLN* 1.3 93.4 - - + +
1346I VAL* 1.3 65.1 + - - +
1347I ALA 3.1 1.1 - - - -
1348I GLU* 3.2 28.7 + - - -
1349I ALA* 2.9 19.9 + - - +
1358I LEU* 5.3 0.2 - - - -
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Residues in contact with VAL1346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I ALA* 4.9 1.5 - - + +
1279I LEU* 4.3 5.8 - - + -
1339I LEU* 4.1 10.3 - - + -
1342I GLU* 2.9 15.6 + - + +
1343I GLN* 3.5 9.0 - - - +
1345I PHE* 1.3 75.8 - - - +
1347I ALA* 1.3 58.0 + - - +
1349I ALA* 3.2 7.4 + - - +
1350I LEU* 3.0 27.4 + - - +
1355I LEU* 4.1 9.3 - - + +
1358I LEU* 4.3 6.3 - - + -
1392I LEU* 3.6 30.5 - - + -
1395I VAL* 4.2 8.1 - - + -
1396I VAL* 4.3 9.2 - - + -
1399I LEU* 3.5 32.3 - - + -
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Residues in contact with ALA1347 (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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1276I ALA 5.7 0.2 - - - +
1279I LEU* 3.8 29.6 - - + +
1343I GLN 2.9 12.2 + - - +
1344I GLN* 3.4 13.2 - - - +
1346I VAL* 1.3 77.6 - - - +
1348I GLU* 1.3 55.1 + - - +
1350I LEU* 3.3 7.0 + - + +
1351I GLU* 2.9 32.3 + - - +
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Residues in contact with GLU1348 (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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365I GLN* 5.1 5.5 - - - +
366I THR* 3.0 29.3 + - + +
1344I GLN* 3.1 15.5 + - - +
1345I PHE* 3.2 32.2 + - - +
1347I ALA* 1.3 75.9 - - - +
1349I ALA* 1.3 61.6 + - - +
1351I GLU* 3.2 7.3 + - - +
1352I LYS* 2.9 27.4 + - - +
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Residues in contact with ALA1349 (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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366I THR* 3.9 9.1 - - + +
367I ASN* 4.8 0.4 - - - +
1345I PHE 2.9 13.1 + - - +
1346I VAL 3.5 7.9 - - - +
1348I GLU* 1.3 75.3 - - - +
1350I LEU* 1.3 53.0 + - - +
1353I GLY* 2.8 30.1 + - - -
1354I THR* 2.8 34.1 + - - +
1355I LEU* 3.7 17.6 + - + -
1358I LEU* 4.0 16.2 - - + -
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Residues in contact with LEU1350 (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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1272I LEU* 4.1 31.0 - - + -
1276I ALA* 3.8 28.5 - - + -
1279I LEU* 4.4 14.6 - - + -
1346I VAL 3.0 13.4 + - - +
1347I ALA* 3.4 9.9 - - + +
1349I ALA* 1.3 76.6 - - - +
1351I GLU* 1.3 64.6 + - + +
1353I GLY* 3.5 7.8 + - - -
1355I LEU* 3.6 29.6 - - + +
1399I LEU* 4.3 17.7 - - + +
1403I ALA* 4.5 5.2 - - + -
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Residues in contact with GLU1351 (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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1347I ALA 2.9 14.3 + - - +
1348I GLU* 3.4 11.0 - - - +
1350I LEU* 1.3 81.3 - - + +
1352I LYS* 1.3 61.4 + - + +
1353I GLY* 3.3 0.9 + - - -
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Residues in contact with LYS1352 (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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362I ALA* 6.4 1.8 - - + -
1348I GLU 2.9 15.9 + - - +
1351I GLU* 1.3 72.1 - - + +
1353I GLY* 1.3 60.8 + - - +
1354I THR* 3.6 15.3 + - - +
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Residues in contact with GLY1353 (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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1349I ALA 2.8 13.2 + - - -
1350I LEU* 3.5 7.4 + - - -
1351I GLU 3.2 4.8 + - - -
1352I LYS* 1.3 75.6 - - - +
1354I THR* 1.3 55.5 + - - -
1355I LEU* 3.5 4.5 - - - -
1356I PRO* 3.8 12.1 - - - +
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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