Contacts of the strand formed by residues 1135 - 1140 (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 ARG1135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955B GLU* 4.2 22.2 + - - +
956B ASN* 4.0 17.2 - - - +
1032B VAL* 5.1 4.6 + - + +
1033B GLN* 5.2 4.0 - - - +
1066B GLU* 2.9 42.5 + - - +
1099B ILE* 5.6 0.7 - - - -
1122B VAL 3.4 2.9 - - - +
1123B ARG* 3.4 2.6 - - - -
1124B VAL* 2.8 40.8 + - + +
1126B MET* 3.4 51.5 - - + +
1127B LEU* 4.7 13.3 - - - +
1128B HIS* 5.0 14.1 - - - +
1133B PHE 3.5 5.8 + - - +
1134B PRO* 1.3 75.5 - - - +
1136B ILE* 1.3 62.4 + - - +
1137B ALA 3.8 0.7 + - - -
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Residues in contact with ILE1136 (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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1032B VAL* 6.1 0.2 - - - -
1066B GLU* 3.2 11.4 - - - +
1067B TYR* 2.8 51.6 + - + +
1087B PHE* 3.8 32.3 - - + -
1088B ASP 4.9 0.2 - - - +
1089B LEU* 3.7 29.6 - - + -
1099B ILE* 4.4 5.6 - - + +
1121B PRO* 3.8 26.7 - - + -
1122B VAL 3.6 2.5 - - - +
1123B ARG* 4.0 32.5 - - + +
1134B PRO* 4.7 1.8 - - + +
1135B ARG* 1.3 73.2 - - - +
1137B ALA* 1.3 59.5 + - - +
1138B PHE* 4.6 4.5 - - + -
11G THR* 5.0 2.7 - - + -
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Residues in contact with ALA1137 (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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1032B VAL* 3.8 25.1 - - + -
1063B PHE* 3.8 8.1 - - + -
1065B CYS 3.9 3.8 - - - -
1066B GLU* 4.4 0.7 - - - +
1120B ILE 3.4 1.7 - - - +
1121B PRO* 3.4 1.4 - - - +
1122B VAL* 2.8 45.6 + - - +
1124B VAL* 3.9 6.7 - - + -
1135B ARG 3.8 0.2 + - - -
1136B ILE* 1.3 72.4 - - - +
1138B PHE* 1.3 63.3 + - - +
1139B PHE* 3.7 22.1 - - + -
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Residues in contact with PHE1138 (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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1063B PHE* 3.5 5.9 - - - -
1064B ILE* 2.9 33.6 + - + -
1065B CYS* 2.8 32.2 + - - +
1067B TYR* 3.8 34.5 - + + -
1087B PHE* 4.4 4.9 - + - -
1108B SER* 3.9 18.4 - - - -
1111B ILE* 4.3 7.2 - - + -
1119B ILE* 3.8 24.7 - - + -
1120B ILE 3.3 3.1 - - - -
1121B PRO* 3.7 32.3 - - + -
1136B ILE* 4.6 2.0 - - + -
1137B ALA* 1.3 72.9 - - - +
1139B PHE* 1.3 61.7 + - - +
1152B PHE* 3.5 45.5 - + - -
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Residues in contact with PHE1139 (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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996B TYR* 3.8 29.4 - + - -
1000B GLY 4.8 0.7 - - - -
1002B LEU* 3.6 28.9 - - + -
1014B ILE* 4.9 1.1 - - + -
1031B VAL* 4.5 2.9 - - + -
1032B VAL* 3.8 21.8 - - + -
1061B GLY 3.5 20.0 - - - -
1062B THR 3.2 5.2 - - - +
1063B PHE* 3.5 26.7 - + + -
1064B ILE* 4.2 0.7 - - - -
1119B ILE* 3.2 4.8 - - - -
1120B ILE* 2.8 38.3 + - + +
1122B VAL* 3.7 31.2 - - + -
1124B VAL* 4.9 0.4 - - + -
1137B ALA* 3.7 20.6 - - + -
1138B PHE* 1.3 77.0 - - - +
1140B SER* 1.3 64.6 + - - +
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Residues in contact with SER1140 (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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1002B LEU* 5.3 1.4 - - - +
1008B LYS* 5.3 1.6 - - - +
1058B ILE* 4.2 7.9 - - - -
1059B PRO 2.7 27.3 + - - -
1060B GLN* 4.2 0.7 - - - +
1061B GLY* 3.0 23.8 + - - -
1062B THR* 3.0 21.6 + - - -
1064B ILE* 3.9 4.8 - - - +
1118B ASN 3.4 7.4 - - - -
1119B ILE* 4.2 3.1 - - - -
1120B ILE* 5.2 1.2 - - - +
1139B PHE* 1.3 74.1 - - - +
1141B SER* 1.3 60.4 + - - +
1142B ARG 3.3 13.7 - - - -
1144B ILE* 3.6 18.8 - - - -
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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