Contacts of the strand formed by residues 1413 - 1417 (chain B) in PDB entry 1W21
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 SER1413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357B LYS* 3.4 17.3 + - - +
1358B GLY* 3.4 30.3 - - - -
1359B PHE* 3.7 7.5 - - - -
1381B TYR* 2.7 45.2 + - - -
1411B GLY 4.6 0.3 + - - -
1412B TYR* 1.3 74.3 - - - +
1414B GLY* 1.3 59.3 + - - +
1431B TYR* 3.3 20.4 - - - -
1432B VAL* 4.5 3.1 - - - -
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Residues in contact with GLY1414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235B SER* 4.6 0.2 - - - -
1286B SER* 3.4 12.6 - - - -
1357B LYS* 4.2 1.1 - - - -
1359B PHE* 3.8 10.2 - - - -
1413B SER* 1.3 76.4 - - - +
1415B ALA* 1.3 61.1 + - - -
1430B PHE* 3.2 6.2 - - - +
1431B TYR* 3.2 52.4 + - - -
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Residues in contact with ALA1415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B LEU 4.9 0.3 - - - +
1235B SER* 4.5 9.6 + - - -
1236B GLU* 3.8 13.2 + - - +
1286B SER* 3.7 16.9 - - - +
1287B CYS 4.0 19.3 + - - +
1288B TYR* 4.6 3.8 - - + -
1359B PHE* 3.8 12.3 - - + +
1360B ALA 5.4 1.1 - - - +
1361B PHE* 3.7 26.7 - - + -
1414B GLY* 1.3 74.9 - - - -
1416B PHE* 1.3 64.0 + - - +
1429B CYS 3.7 4.9 - - - -
1430B PHE* 4.6 0.4 - - - +
1431B TYR* 5.0 1.1 - - - -
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Residues in contact with PHE1416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B LEU* 3.6 28.3 - - + -
1128B LEU* 3.4 58.1 - - + +
1130B CYS* 4.0 25.4 - - - -
1135B CYS* 4.7 1.6 - - - -
1236B GLU* 3.4 14.1 - - - +
1287B CYS 5.0 2.0 - - - -
1361B PHE* 4.4 0.2 - - - -
1415B ALA* 1.3 76.8 - - - +
1417B ILE* 1.4 68.0 + - - +
1418B ASP* 6.0 0.2 - - + -
1429B CYS* 3.0 63.6 + - + +
1430B PHE* 3.7 23.1 - - - -
1431B TYR* 4.1 7.4 - + + -
1453B ALA* 4.2 3.6 - - + -
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Residues in contact with ILE1417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B LEU* 4.0 26.0 - - + -
1130B CYS* 4.0 14.5 + - - +
1236B GLU* 3.3 10.5 + - - +
1288B TYR* 3.9 18.8 - - + -
1289B GLY 4.1 2.9 - - - +
1361B PHE* 4.2 4.5 - - + -
1416B PHE* 1.4 83.2 - - - +
1418B ASP* 1.3 73.7 + - - +
1419B TYR* 3.0 52.8 + - + +
1420B TRP* 4.8 0.2 - - - -
1426B PHE* 3.8 20.4 - - + -
1427B ASN 3.5 25.1 - - - +
1428B PRO* 4.1 4.0 - - + -
1429B CYS* 4.8 0.9 - - - -
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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