Contacts of the strand formed by residues 1043 - 1050 (chain B) in PDB entry 5JP2
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 THR1043 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B GLN* 4.1 19.7 - - + +
1042B LEU* 1.3 79.3 - - - +
1044B SER* 1.3 73.9 + - - +
1045B VAL* 3.1 3.8 + - - -
1079B ASN* 3.5 25.4 - - - +
1113B PHE* 3.4 2.9 - - - +
1114B VAL* 2.9 49.1 + - - +
1115B GLY* 4.8 2.2 - - - -
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Residues in contact with SER1044 (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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1043B THR* 1.3 78.7 + - - +
1045B VAL* 1.3 62.7 + - - +
1046B GLN* 3.5 13.3 + - - +
1079B ASN* 3.9 5.7 + - - -
1112B GLN* 3.4 12.0 - - - +
1113B PHE* 3.8 3.3 - - - -
1114B VAL* 4.5 18.0 - - - +
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Residues in contact with VAL1045 (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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1011B LEU* 5.2 2.0 - - + -
1042B LEU* 3.4 36.8 - - + +
1043B THR* 3.8 3.8 - - - +
1044B SER* 1.3 74.9 - - - +
1046B GLN* 1.3 68.3 + - - +
1076B LYS* 3.7 1.6 - - - +
1077B LEU* 3.0 62.7 + - + +
1078B ALA 4.2 9.6 - - - +
1079B ASN* 4.5 1.5 + - - -
1080B LEU* 4.1 17.0 - - + -
1111B VAL* 4.8 9.0 - - + -
1112B GLN 3.2 10.3 - - - +
1113B PHE* 4.0 9.0 - - + -
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Residues in contact with GLN1046 (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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1044B SER* 4.0 11.1 + - - +
1045B VAL* 1.3 79.3 - - - +
1047B VAL* 1.3 66.9 + - - +
1048B LEU* 4.5 2.2 - - + +
1074B LEU* 3.8 22.7 - - + +
1075B TRP 3.2 11.9 - - - +
1076B LYS* 3.6 32.4 - - + +
1077B LEU 4.8 0.2 - - - +
1110B ALA 3.9 0.2 - - - +
1111B VAL* 3.4 5.2 - - - +
1112B GLN* 2.8 59.5 + - + +
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Residues in contact with VAL1047 (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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1028B LEU* 4.2 17.3 - - + -
1030B TYR* 5.8 0.9 - - + -
1045B VAL* 5.3 0.2 - - + -
1046B GLN* 1.3 79.9 - - - +
1048B LEU* 1.3 64.9 + - - +
1073B LEU 3.6 1.0 - - - +
1074B LEU* 3.4 4.2 - - - +
1075B TRP* 2.8 56.7 + - + -
1077B LEU* 4.1 25.8 - - + -
1092B LEU* 4.4 9.9 - - + -
1109B LEU* 3.8 27.6 - - + -
1110B ALA 3.3 8.5 - - - +
1111B VAL* 4.2 16.6 - - + -
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Residues in contact with LEU1048 (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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1046B GLN* 5.2 0.4 - - - +
1047B VAL* 1.3 80.6 - - - +
1049B LEU* 1.3 62.0 + - - +
1050B PRO* 3.6 6.8 - - + +
1072B ARG* 5.6 10.5 - - + -
1073B LEU 3.4 4.7 - - - +
1074B LEU* 3.7 22.2 - - + -
1109B LEU* 3.5 9.4 - - - +
1110B ALA* 2.8 52.6 + - + +
1112B GLN* 3.6 39.0 - - + +
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Residues in contact with LEU1049 (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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1026B VAL* 4.0 13.7 - - + -
1047B VAL 4.3 0.2 - - - -
1048B LEU* 1.3 74.0 - - - +
1050B PRO* 1.3 75.0 - - - +
1051B LEU* 3.9 13.5 + - + +
1072B ARG* 3.5 2.1 - - - -
1073B LEU* 2.8 44.9 + - + +
1075B TRP* 4.1 13.4 - - + -
1094B ALA* 4.1 14.4 - - + -
1096B TRP* 4.0 24.9 - - + -
1107B PRO* 4.2 21.1 - - + -
1108B SER 3.9 14.6 - - - +
1109B LEU* 3.8 19.1 - - + -
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Residues in contact with PRO1050 (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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1048B LEU* 3.6 9.2 - - + +
1049B LEU* 1.3 90.1 - - + +
1051B LEU* 1.3 72.6 + - - +
1071B ARG 3.9 7.2 - - - +
1072B ARG* 4.3 8.2 - - + -
1107B PRO* 5.5 2.4 - - - +
1108B SER* 3.5 25.1 + - - +
1110B ALA* 5.5 1.8 - - + +
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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