Contacts of the strand formed by residues 1293 - 1300 (chain D) in PDB entry 6CET
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 TRP1293 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D TYR* 4.0 8.7 + - - -
320D HIS* 5.4 5.4 - - - -
321D TYR* 3.8 21.4 - - + +
324D ARG* 3.7 35.9 - - + +
989D PHE* 3.6 54.1 - + + -
990D VAL* 4.7 9.6 - - + -
1291D ARG* 3.9 16.2 - - + -
1292D LYS* 1.3 72.8 - - - +
1294D PHE* 1.3 61.0 + - - +
1295D GLU* 4.8 0.7 - - - +
1389D HIS* 3.5 1.4 - - - +
1390D TRP* 2.9 93.7 + + + +
1391D MET* 4.0 11.4 - - + -
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Residues in contact with PHE1294 (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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321D TYR* 3.8 12.3 + + - -
322D ILE* 2.9 67.0 - - + +
323D ASN* 3.9 2.5 - - - -
324D ARG* 4.0 2.2 + - - +
1292D LYS* 3.2 55.1 + - + -
1293D TRP* 1.3 74.4 - - - +
1295D GLU* 1.3 71.2 + - - +
1296D VAL* 5.7 0.7 - - + -
1387D LYS* 3.8 19.3 - - - -
1388D LEU 3.1 13.2 - - - +
1389D HIS* 3.4 20.6 - + + -
1421D GLU* 5.7 1.3 - - + -
1430D LEU* 5.2 7.0 - - + -
1431D TYR* 4.3 18.4 - + - -
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Residues in contact with GLU1295 (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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323D ASN* 5.0 6.1 - - - +
324D ARG* 3.3 43.3 - - - +
326D PHE* 4.3 25.4 - - + -
1294D PHE* 1.3 80.7 + - - +
1296D VAL* 1.3 71.0 + - - +
1387D LYS* 3.8 3.9 + - - -
1388D LEU* 2.9 47.1 + - + +
1390D TRP* 3.2 34.0 + - - -
1418D PRO* 6.4 1.6 - - + -
1553D MET* 6.1 1.6 - - + -
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Residues in contact with VAL1296 (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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323D ASN* 5.1 1.0 + - - +
1294D PHE* 5.7 0.2 - - + -
1295D GLU* 1.3 78.9 - - - +
1297D ALA* 1.3 65.2 + - - +
1298D PHE* 3.5 33.2 - - + -
1385D GLU* 4.8 4.5 - - + -
1386D ILE 3.8 5.8 - - - +
1387D LYS* 3.4 38.6 - - + +
1388D LEU* 5.0 0.9 - - - -
1418D PRO* 3.5 7.0 - - - +
1419D VAL 2.9 37.5 + - - +
1421D GLU* 3.5 31.9 - - + +
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Residues in contact with ALA1297 (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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1295D GLU 4.4 0.2 - - - -
1296D VAL* 1.3 74.7 - - - +
1298D PHE* 1.3 63.2 + - - +
1384D PHE 4.7 0.2 - - - -
1385D GLU* 3.4 6.4 - - - +
1386D ILE* 2.9 43.6 + - + +
1388D LEU* 4.4 11.8 - - + +
1402D VAL* 5.8 7.4 - - + -
1405D TRP* 6.4 2.5 - - + -
1416D LEU* 3.8 22.0 - - + -
1417D VAL 3.7 6.3 - - - +
1418D PRO* 4.1 7.0 - - + -
1419D VAL 4.5 0.2 - - - +
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Residues in contact with PHE1298 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1296D VAL* 3.5 20.9 - - + -
1297D ALA* 1.3 77.9 - - - +
1299D VAL* 1.3 63.4 + - - +
1300D ALA* 4.2 2.6 + - + -
1383D ALA* 3.8 22.2 - - + -
1384D PHE 3.5 2.0 - - - -
1385D GLU* 3.2 37.5 - - + -
1416D LEU* 3.3 4.6 - - - +
1417D VAL* 2.9 38.3 + - + +
1419D VAL* 3.6 36.6 - - + -
1421D GLU* 4.7 5.4 - - - -
1490D SER* 3.9 28.3 - - - -
1492D PHE* 5.5 7.6 - - + -
1501D GLN* 5.6 2.0 - - - -
1503D ILE* 5.0 9.6 - - + -
1510D PHE* 6.1 1.6 - + - -
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Residues in contact with VAL1299 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1093D PHE* 5.2 14.4 - - + -
1096D PHE* 5.1 4.3 - - + -
1297D ALA 5.7 0.2 - - - +
1298D PHE* 1.3 77.3 - - - +
1300D ALA* 1.3 59.4 + - - +
1382D ALA 4.3 2.1 - - - +
1383D ALA* 3.3 9.2 - - - +
1384D PHE* 2.8 64.8 + - + +
1386D ILE* 5.1 7.2 - - + -
1414D PHE* 3.7 33.3 - - + +
1415D LEU 3.2 14.8 - - - +
1416D LEU* 3.8 18.6 - - + -
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Residues in contact with ALA1300 (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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1298D PHE* 4.2 3.1 + - + +
1299D VAL* 1.3 74.9 - - - +
1301D GLU* 1.3 63.2 + - - +
1302D GLU* 3.4 2.3 - - - +
1382D ALA 5.6 1.3 - - - -
1383D ALA* 5.2 6.1 - - + +
1414D PHE* 3.6 6.3 - - - -
1415D LEU* 2.9 40.3 + - + +
1488D SER* 5.4 7.0 - - - +
1503D ILE* 5.7 7.4 - - + -
1504D HIS 5.2 2.5 - - - +
1505D VAL* 4.9 7.2 - - + -
1506D THR* 4.6 18.8 - - - +
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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