Contacts of the strand formed by residues 1040 - 1044 (chain B) in PDB entry 5JHN
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 LEU1040 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B VAL* 5.8 0.4 - - - +
934B PRO 4.4 2.9 + - - +
935B ILE* 3.9 20.9 - - + +
936B PRO* 3.5 22.0 - - - +
1036B ILE* 4.7 6.5 - - + -
1038B VAL* 3.5 31.0 + - + +
1039B ARG* 1.3 78.8 - - - +
1041B GLN* 1.3 61.8 + - - +
1052B VAL* 4.2 15.3 - - + -
1053B ARG 3.4 9.4 - - - +
1054B ALA* 4.4 4.9 - - - -
1055B LEU* 4.2 4.7 - - - +
1058B ILE* 4.9 2.0 - - + -
1064B ILE* 4.2 21.8 - - + +
1065B CYS* 4.7 4.0 - - + -
1107B ILE* 4.6 19.7 - - + -
1150B LEU* 3.5 26.9 - - + -
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Residues in contact with GLN1041 (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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921B ILE* 5.2 2.6 - - - +
935B ILE* 4.4 2.0 - - - -
936B PRO* 3.6 20.6 - - + +
938B VAL* 3.5 30.1 - - + +
1040B LEU* 1.3 78.2 - - - +
1042B LEU* 1.3 71.5 + - - +
1043B TYR* 3.7 2.9 + - - +
1052B VAL* 3.3 7.7 - - - -
1053B ARG* 2.6 75.8 + - + +
1055B LEU* 3.8 31.3 - - + +
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Residues in contact with LEU1042 (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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926B VAL* 3.9 22.0 - - + -
935B ILE* 4.3 2.9 - - + +
936B PRO 2.9 13.8 + - - +
937B CYS* 3.1 24.1 - - + -
938B VAL 2.9 24.5 + - - -
947B PRO* 4.0 20.9 - - + -
1041B GLN* 1.3 74.5 - - - +
1043B TYR* 1.3 61.0 + - - +
1050B TRP* 4.0 11.0 - - + -
1051B GLY 3.4 15.9 - - - +
1052B VAL* 4.7 0.7 - - - +
1107B ILE* 4.2 11.7 - - + -
1110B PHE* 3.4 47.6 - - + -
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Residues in contact with TYR1043 (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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938B VAL* 3.2 24.7 - - + -
1041B GLN* 3.9 7.6 - - - +
1042B LEU* 1.3 77.6 - - - +
1044B ARG* 1.3 82.3 + - - +
1045B THR* 3.5 15.9 + - + +
1050B TRP* 3.4 8.7 - - - -
1051B GLY* 2.9 62.1 + - - -
1052B VAL 3.8 3.4 - - - -
1053B ARG* 3.6 58.3 - - + +
1149B GLU* 3.2 34.9 + - + +
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Residues in contact with ARG1044 (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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938B VAL* 3.3 5.9 + - - +
939B ASN* 3.3 42.5 - - + +
940B GLY 5.3 1.3 + - - +
941B VAL* 3.3 22.0 - - + +
942B ASP* 3.0 29.4 + - - +
944B GLU* 3.7 26.3 + - - +
1043B TYR* 1.3 83.7 - - - +
1045B THR* 1.3 69.6 + - - +
1049B GLY* 3.5 25.3 - - - -
1050B TRP* 3.2 44.1 - - + +
1205B SAM 4.8 0.4 + - - -
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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