Contacts of the strand formed by residues 1415 - 1418 (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 LEU1415 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1299D VAL* 3.2 8.9 - - - +
1300D ALA* 2.9 43.2 + - + +
1302D GLU* 3.3 22.7 - - + +
1406D HIS* 3.9 13.9 - - + +
1409D ALA* 4.3 3.1 - - - -
1410D THR* 3.9 29.2 - - + -
1414D PHE* 1.3 71.2 - - - +
1416D LEU* 1.3 74.6 + - - +
1417D VAL* 3.7 28.0 - - + -
1506D THR* 3.7 29.6 - - - +
1558D TRP 5.9 0.4 - - - +
1560D SER* 5.7 5.4 - - - +
1562D ALA* 5.9 1.6 - - + -
1563D THR* 4.9 6.3 - - + -
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Residues in contact with LEU1416 (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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1093D PHE* 6.0 3.4 - - + -
1297D ALA* 3.8 24.0 - - + -
1298D PHE 3.3 17.9 - - - +
1299D VAL* 3.8 18.6 - - + -
1386D ILE* 5.4 5.8 - - + -
1402D VAL* 4.5 7.0 - - + +
1405D TRP* 3.7 38.1 - - + +
1406D HIS* 3.3 35.4 - - + +
1409D ALA* 4.0 13.8 - - + +
1414D PHE 5.2 0.2 - - - +
1415D LEU* 1.3 81.2 - - - +
1417D VAL* 1.3 69.5 + - - +
1558D TRP* 3.6 10.2 - - + -
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Residues in contact with VAL1417 (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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1297D ALA* 4.5 3.1 - - - -
1298D PHE* 2.9 32.4 + - + +
1415D LEU* 3.7 19.7 - - + +
1416D LEU* 1.3 81.2 - - - +
1418D PRO* 1.3 84.1 - - + +
1419D VAL* 3.6 9.3 + - + +
1506D THR* 5.6 6.1 - - - +
1507D GLY 5.3 5.4 - - - +
1551D ASN* 4.2 9.0 - - - +
1554D LEU* 4.2 27.4 - - + -
1558D TRP* 4.6 8.7 - - + -
1563D THR* 5.1 6.5 - - + -
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Residues in contact with PRO1418 (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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326D PHE* 5.3 11.9 - - + -
1295D GLU* 6.4 1.6 - - + -
1296D VAL 3.5 11.0 - - - +
1297D ALA* 4.1 6.4 - - + -
1402D VAL* 6.2 0.7 - - + -
1416D LEU* 5.9 0.2 - - + -
1417D VAL* 1.3 97.5 - - + +
1419D VAL* 1.3 59.6 + - - +
1551D ASN* 3.3 7.3 - - - +
1553D MET* 3.5 37.8 - - + +
1558D TRP* 3.5 49.8 - - + +
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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