Contacts of the strand formed by residues 1066 - 1074 (chain B) in PDB entry 1Q6S
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 TYR1066 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1034B VAL* 3.7 19.3 - - + -
1035B ALA* 3.3 27.1 - - + +
1040B ASN* 3.5 27.1 - - + +
1043B ARG* 2.8 47.9 + - + -
1044B ASN* 2.5 37.0 + - - -
1051B PRO* 3.0 34.7 - - + +
1056B ARG* 4.0 10.5 - - - +
1059B LEU* 3.6 4.6 - - - +
1064B ASN* 2.9 18.6 + - - +
1065B ASP* 1.3 82.7 + - - +
1067B ILE* 1.3 67.1 + - - +
1068B ASN* 3.5 16.4 - - - -
1094B HIS* 4.7 1.7 - - - -
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Residues in contact with ILE1067 (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 ARG* 5.4 2.2 - - - -
1051B PRO* 4.3 1.4 - - - +
1056B ARG* 4.9 1.0 - - - +
1057B ILE* 3.4 28.9 + - + +
1059B LEU* 3.7 22.9 - - + -
1065B ASP 3.7 0.4 + - - -
1066B TYR* 1.3 91.2 - - - +
1068B ASN* 1.3 69.5 + - - +
1069B ALA* 2.9 20.4 + - + +
1084B THR* 4.3 5.2 - - - +
1085B GLN* 6.1 2.0 - - + +
1091B THR* 5.2 6.5 - - + +
1094B HIS* 4.0 13.7 - - + +
1095B PHE* 4.0 26.2 - - + +
1098B MET* 3.8 27.8 - - + -
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Residues in contact with ASN1068 (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 ARG 4.1 3.3 + - - +
1044B ASN* 3.0 20.9 + - - +
1045B ARG 4.9 0.2 - - - +
1046B TYR 5.6 0.2 - - - +
1049B VAL* 3.0 28.3 + - - +
1051B PRO* 3.7 9.2 - - - +
1066B TYR* 3.5 16.3 + - - +
1067B ILE* 1.3 73.6 - - - +
1069B ALA* 1.3 52.2 + - - +
1084B THR* 2.6 27.8 + - - -
1085B GLN* 3.4 35.5 + - - +
1257B ARG* 2.8 35.2 + - - +
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Residues in contact with ALA1069 (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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1051B PRO* 3.6 4.8 - - - +
1056B ARG* 3.3 7.6 - - - +
1057B ILE* 3.0 29.6 + - + -
1067B ILE* 2.9 9.7 + - + -
1068B ASN* 1.3 75.3 + - - +
1070B SER* 1.3 65.5 + - - +
1082B ILE* 4.0 1.6 - - + -
1083B LEU 3.2 8.1 - - - +
1084B THR* 3.4 15.7 - - - +
1098B MET* 3.4 31.4 - - + -
1257B ARG* 4.2 1.3 - - - +
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Residues in contact with SER1070 (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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1051B PRO* 3.4 13.8 - - - +
1055B SER* 3.4 9.0 - - - -
1057B ILE* 4.3 4.7 - - - -
1069B ALA* 1.3 74.7 - - - +
1071B LEU* 1.3 60.5 + - - +
1072B ILE* 3.5 11.9 - - - +
1082B ILE* 3.2 4.3 - - - -
1083B LEU 2.8 30.6 + - - -
1256B PHE 3.5 21.5 + - - -
1257B ARG* 2.9 33.6 + - - +
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Residues in contact with LEU1071 (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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1055B SER* 2.7 22.7 + - - +
1056B ARG 5.6 0.2 - - - +
1057B ILE* 3.7 18.3 - - + +
1070B SER* 1.3 72.4 - - - +
1072B ILE* 1.3 63.5 + - - +
1073B LYS* 4.6 15.6 - - + +
1080B SER* 4.0 16.6 - - - +
1081B TYR 3.6 12.1 - - - +
1082B ILE* 4.1 3.1 - - + +
1102B GLN* 6.1 0.7 - - - +
1210B PRO* 4.0 24.2 - - + -
1256B PHE* 3.4 21.5 - - - +
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Residues in contact with ILE1072 (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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1070B SER* 3.5 25.4 - - - +
1071B LEU* 1.3 77.5 - - - +
1073B LYS* 1.3 59.6 + - - +
1074B MET* 3.7 29.6 + - + -
1079B ARG 4.0 0.3 - - - +
1080B SER* 3.1 4.3 - - - -
1081B TYR* 2.7 50.5 + - + +
1083B LEU* 4.0 21.5 - - + -
1253B MET* 3.8 21.5 - - + +
1256B PHE* 3.7 25.1 - - + -
1257B ARG* 4.0 10.1 - - + -
1260B LEU* 4.6 8.5 - - + -
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Residues in contact with LYS1073 (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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1071B LEU* 3.7 17.6 + - + -
1072B ILE* 1.3 72.7 - - - +
1074B MET* 1.3 66.4 + - - +
1075B GLU* 3.5 21.6 + - + +
1079B ARG 4.9 0.4 - - - +
1080B SER* 3.4 20.6 - - - +
1252B GLU* 5.1 1.2 - - - +
1256B PHE* 3.4 33.1 - - + -
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Residues in contact with MET1074 (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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1072B ILE* 3.7 18.6 - - + -
1073B LYS* 1.3 75.6 - - - +
1075B GLU* 1.3 59.6 + - - +
1076B GLU 3.6 2.0 - - - -
1077B ALA* 4.0 16.8 - - + +
1078B GLN* 2.8 26.2 + - - -
1079B ARG 2.8 24.2 + - - +
1081B TYR* 4.2 2.7 - - + -
1230B THR* 3.7 20.6 - - + +
1234B LEU* 6.0 0.4 - - + -
1249B VAL* 3.7 26.0 - - + +
1252B GLU* 3.9 28.3 - - + -
1253B MET* 3.6 33.4 - - + -
1256B PHE* 4.6 1.6 - - - -
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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