Contacts of the strand formed by residues 1598 - 1601 (chain B) in PDB entry 6X34
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 GLN1598 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245B PHE* 3.4 12.8 - - + +
1246B GLU* 3.3 21.5 - - - +
1247B ALA* 4.7 4.5 - - + +
1248B VAL* 4.1 1.2 - - - +
1288B PHE 3.9 0.2 - - - +
1289B LEU* 3.5 12.6 - - - +
1290B ARG* 2.6 67.5 + - + +
1291B LEU 3.4 9.0 + - - +
1292B SER* 3.5 25.9 - - - +
1596B GLU* 3.7 11.4 - - + +
1597B MET* 1.3 76.1 - - - +
1599B MET* 1.3 61.6 + - - +
1644B GLU* 3.8 13.7 + - - -
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Residues in contact with MET1599 (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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1245B PHE* 4.0 4.3 - - - -
1246B GLU* 2.9 30.4 + - + +
1247B ALA 5.6 4.9 - - - +
1248B VAL* 3.7 20.4 - - + +
1252B HIS* 6.0 3.6 - - - -
1255B TYR* 5.0 24.5 - - + +
1287B LEU* 4.9 13.5 - - + -
1288B PHE 3.6 9.9 - - - +
1289B LEU* 5.4 4.5 - - + -
1598B GLN* 1.3 74.7 - - - +
1600B LEU* 1.3 85.6 + - - +
1601B MET* 3.4 11.9 + - + -
1602B PRO* 5.5 2.5 - - + -
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Residues in contact with LEU1600 (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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1243B PRO* 3.8 12.1 - - + +
1244B GLN* 3.5 37.5 - - - +
1245B PHE* 3.6 33.4 - - + +
1288B PHE* 3.4 43.1 + - + +
1457B TYR* 5.0 5.4 - - + +
1458B HIS* 6.1 0.2 - - - -
1459B GLN 4.0 6.7 - - - +
1460B HIS* 3.7 34.3 + - + -
1599B MET* 1.3 88.6 - - - +
1601B MET* 1.3 64.6 + - - +
1602B PRO* 4.0 4.3 - - - +
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Residues in contact with MET1601 (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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1243B PRO* 3.3 23.0 - - - +
1244B GLN* 3.3 19.2 + - - +
1246B GLU* 5.1 9.6 - - + -
1460B HIS* 5.5 0.2 - - - -
1599B MET* 3.4 13.1 + - + +
1600B LEU* 1.3 75.0 - - - +
1602B PRO* 1.3 70.4 - - + +
1603B VAL 4.1 14.8 - - - +
1604B SER* 5.5 2.2 - - - -
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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