Contacts of the strand formed by residues 1047 - 1056 (chain B) in PDB entry 6XRA
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 TYR1047 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1034A LEU 3.7 18.9 + - - -
1035A GLY* 5.0 0.7 - - - -
715B PRO* 4.0 19.9 - - + +
718B PHE* 4.4 4.7 - + - -
1038B LYS 5.4 4.9 - - - -
1039B ARG 4.9 4.3 - - - -
1040B VAL* 3.0 38.5 - - + +
1045B LYS 4.0 0.4 + - - -
1046B GLY* 1.3 74.6 - - - -
1048B HIS* 1.3 61.4 + - - +
1066B THR* 3.1 7.9 - - - -
1067B TYR* 2.9 77.0 + + + +
1069B PRO* 4.5 12.8 - - + -
1107B ARG 5.2 0.2 + - - -
1108B ASN* 3.3 42.2 - - + +
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Residues in contact with HIS1048 (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 CYS* 3.3 35.4 - - - +
1035B GLY 4.1 0.9 - - - -
1036B GLN* 2.9 35.6 + - - +
1037B SER* 3.1 41.6 + - - +
1039B ARG 4.9 3.5 + - - +
1042B PHE 4.8 3.6 + - - +
1043B CYS* 3.7 29.6 - - + +
1047B TYR* 1.3 73.3 - - - +
1049B LEU* 1.3 66.3 + - - +
1050B MET* 3.4 19.1 + - - -
1051B SER* 2.8 27.3 + - - -
1064B HIS* 4.7 0.2 - - + -
1065B VAL 4.0 3.1 - - - -
1066B THR* 4.1 4.3 - - + -
1067B TYR* 4.7 3.6 + - - -
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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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720B ILE* 3.4 33.2 - - + -
1035B GLY 5.2 0.2 - - - +
1036B GLN* 3.6 27.9 + - - +
1047B TYR 3.8 0.2 + - - -
1048B HIS* 1.3 78.9 - - - +
1050B MET* 1.3 61.8 + - - +
1065B VAL* 2.9 18.8 + - + +
1066B THR* 4.3 3.6 - - - -
1067B TYR* 3.8 36.1 - - + -
1079C PRO* 3.7 27.4 - - + +
1089C PHE* 4.0 5.6 - - + -
1090C PRO* 4.0 33.0 - - + +
1093C GLY 4.8 1.8 - - - +
1094C VAL* 4.1 13.0 - - + +
1107C ARG* 5.2 1.2 - - - -
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Residues in contact with MET1050 (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 CYS 4.7 0.4 - - - -
1035B GLY 5.7 1.1 - - - -
1048B HIS* 3.4 9.0 + - - -
1049B LEU* 1.3 79.9 - - - +
1051B SER* 1.3 70.4 + - - +
1052B PHE* 3.8 19.5 - - + -
1065B VAL* 2.8 28.4 + - - +
710C ASN* 4.8 0.4 - - - +
712C ILE* 3.3 32.8 - - + -
1077C THR* 3.9 17.5 - - - +
1078C ALA 4.0 2.2 - - - +
1079C PRO* 3.8 41.5 - - + -
1094C VAL* 3.6 36.3 - - + -
1107C ARG* 5.7 5.2 - - - +
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Residues in contact with SER1051 (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 CYS* 3.4 22.8 + - - +
1033B VAL* 4.3 19.5 - - - +
1048B HIS* 2.8 17.3 + - - -
1050B MET* 1.3 83.2 + - - +
1052B PHE* 1.3 76.9 + - - +
1053B PRO* 4.3 5.1 - - - +
1062B PHE* 5.4 2.9 - - - -
1063B LEU 3.2 10.3 - - - -
1064B HIS* 3.3 23.8 - - - -
712C ILE* 5.5 1.2 - - - +
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Residues in contact with PHE1052 (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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1033B VAL* 5.0 0.2 - - - -
1050B MET* 3.8 23.1 - - + -
1051B SER* 1.3 84.7 - - - +
1053B PRO* 1.3 69.1 - - + +
1054B GLN 3.9 0.3 + - - -
1062B PHE* 4.7 1.1 - - - -
1063B LEU* 2.9 59.3 + - + +
1065B VAL* 3.7 25.6 - - + -
705C VAL* 3.9 25.4 - - + -
708C SER* 5.2 2.7 - - - -
710C ASN* 3.0 39.0 - - - -
712C ILE* 4.1 13.7 - - + -
1079C PRO* 4.4 7.4 - - + -
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Residues in contact with PRO1053 (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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1029B MET* 3.9 30.3 - - + -
1033B VAL* 3.7 23.8 - - + -
1052B PHE* 1.3 86.9 - - + +
1054B GLN* 1.3 60.8 + - - +
1060B VAL* 4.2 8.3 - - + -
1061B VAL 3.5 6.3 - - - +
1062B PHE* 4.0 20.6 - - + -
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Residues in contact with GLN1054 (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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724B THR* 5.6 2.0 - - - +
1052B PHE 4.9 0.6 - - - +
1053B PRO* 1.3 74.6 - - - +
1055B SER* 1.3 66.1 + - - +
1060B VAL* 3.7 5.5 - - - -
1061B VAL* 2.8 62.8 + - + +
1063B LEU* 3.3 35.0 - - - +
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Residues in contact with SER1055 (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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1054B GLN* 1.3 83.5 + - - +
1056B ALA* 1.3 67.0 + - - +
1059B GLY 3.8 7.6 - - - -
1060B VAL* 4.7 1.6 - - - +
1061B VAL* 5.1 1.1 - - - +
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Residues in contact with ALA1056 (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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726B ILE* 5.8 3.1 - - + -
1055B SER* 1.3 79.5 - - - +
1057B PRO* 1.3 77.8 - - + +
1058B HIS 3.1 3.6 + - - +
1059B GLY* 3.1 29.0 + - - +
1061B VAL* 4.2 17.3 - - + -
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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