Contacts of the strand formed by residues 1038 - 1043 (chain B) in PDB entry 3KQ4
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 ASN1038 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B THR* 5.2 5.1 - - - +
941B GLY 3.0 23.4 + - - +
942B THR* 3.2 25.3 + - - +
972B LEU* 3.3 2.9 - - - -
973B MET* 2.7 54.2 + - + +
974B PHE 4.5 0.4 - - - +
975B GLU* 4.1 23.9 - - - +
1036B LEU* 4.4 2.4 - - - +
1037B ILE* 1.3 77.3 - - - +
1039B TYR* 1.3 62.3 + - - +
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Residues in contact with TYR1039 (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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936B LEU* 3.8 20.3 - - + +
938B GLU* 2.7 28.0 + - - +
939B SER 3.6 15.7 - - - -
940B THR* 3.5 11.4 + - - +
941B GLY* 3.3 59.2 + - - +
942B THR* 4.3 2.7 - - - -
943B ILE* 5.1 10.1 - - + -
962B ILE* 3.2 33.3 - - + +
964B VAL* 5.5 4.5 - - + -
970B ILE* 3.7 17.3 - - + -
971B HIS 2.9 14.4 - - - +
972B LEU* 3.7 18.6 - - + -
973B MET* 4.5 2.9 - - - +
1037B ILE 5.3 0.2 - - - +
1038B ASN* 1.3 81.3 + - - +
1040B GLU* 1.3 70.3 + - - +
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Residues in contact with GLU1040 (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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939B SER 3.3 11.0 - - - +
940B THR* 4.5 9.5 - - + +
969B LEU 3.7 1.2 - - - +
970B ILE* 3.7 2.2 - - - -
971B HIS* 2.9 64.8 + - + +
973B MET* 4.2 9.4 - - - +
1039B TYR* 1.3 82.9 - - - +
1041B ALA* 1.3 71.1 + - - +
1042B ILE* 4.1 7.9 - - + +
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Residues in contact with ALA1041 (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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939B SER* 2.9 25.1 + - - +
964B VAL* 3.5 30.7 - - + -
965B GLN* 5.9 0.2 - - + -
968B HIS* 4.3 10.3 - - + -
969B LEU 3.5 6.3 - - - -
1039B TYR* 5.1 0.2 - - - -
1040B GLU* 1.3 79.9 - - - +
1042B ILE* 1.3 67.8 + - - +
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Residues in contact with ILE1042 (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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968B HIS* 3.3 6.3 - - - -
969B LEU* 2.7 55.0 + - + +
971B HIS* 3.4 35.0 - - + +
1014B THR* 5.5 5.6 - - + +
1040B GLU* 4.1 10.8 - - - +
1041B ALA* 1.3 84.2 - - - +
1043B SER* 1.3 75.5 + - - +
1047B ALA* 4.0 12.6 - - + -
1049B LEU* 6.3 2.2 - - + -
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Residues in contact with SER1043 (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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967B ASN* 4.3 3.1 + - - -
968B HIS* 3.6 26.3 - - - -
1042B ILE* 1.3 75.6 - - - +
1044B ALA* 1.3 62.8 + - - +
1045B ALA* 3.3 17.2 + - - +
1046B THR* 3.9 19.7 + - - -
1047B ALA* 3.0 25.3 + - - +
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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