Contacts of the strand formed by residues 1416 - 1420 (chain D) in PDB entry 5E18
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 ALA1416 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1381D VAL* 3.6 3.3 - - - +
1382D THR* 2.7 41.7 + - - +
1383D ASP* 3.0 31.6 + - + +
1414D PRO 3.6 4.4 + - - +
1415D VAL* 1.3 71.0 - - - +
1417D TRP* 1.3 53.4 + - - +
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Residues in contact with TRP1417 (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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1379D VAL* 3.6 33.7 - - + -
1380D GLU 3.3 15.0 - - - +
1381D VAL* 4.4 3.1 - - + -
1382D THR* 3.5 6.3 + - - -
1397D LYS* 4.4 17.0 - - + -
1400D VAL* 3.9 27.8 - - + +
1401D GLU* 4.0 27.3 - - + +
1404D ASN* 3.8 15.5 - - - +
1415D VAL* 3.1 24.9 - - + -
1416D ALA* 1.3 73.9 - - - +
1418D LYS* 1.3 65.1 + - - +
1419D PRO* 4.1 18.5 - - + +
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Residues in contact with LYS1418 (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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1337D GLU* 4.1 30.3 + - + +
1379D VAL* 3.3 6.9 - - - +
1380D GLU* 2.8 58.1 + - + +
1382D THR* 4.0 21.4 - - + +
1417D TRP* 1.3 80.1 - - - +
1419D PRO* 1.3 89.5 - - + +
1420D LEU* 5.6 2.9 - - + -
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Residues in contact with PRO1419 (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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1336D LEU* 3.5 30.6 - - + +
1337D GLU* 6.4 0.4 - - - -
1340D GLY* 5.6 0.7 - - - -
1341D PRO* 3.9 32.1 - - + -
1376D MET* 4.7 5.2 - - + -
1379D VAL* 4.4 4.0 - - + -
1397D LYS* 6.5 0.9 - - - -
1417D TRP* 4.3 18.4 - - + +
1418D LYS* 1.3 107.8 - - + +
1420D LEU* 1.3 60.6 - - - +
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Residues in contact with LEU1420 (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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1333D HIS* 6.1 1.3 - - - +
1336D LEU* 4.0 2.7 - - + +
1375D MET 3.8 9.7 - - - +
1376D MET* 4.2 8.6 - - - +
1378D TYR* 2.9 36.0 + - - +
1379D VAL* 3.7 9.0 - - - +
1380D GLU* 4.0 24.0 - - + +
1394D VAL* 3.7 40.4 - - + -
1418D LYS* 4.4 2.9 - - + +
1419D PRO* 1.3 78.3 - - - +
1421D LEU* 1.3 65.1 + - - +
1422D MET* 3.9 20.9 + - + +
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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