Contacts of the strand formed by residues 1105 - 1111 (chain B) in PDB entry 3F66
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 ILE1105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1306A GLU 5.8 0.9 - - - -
1307A TYR* 3.5 38.8 - - + +
1096B THR* 3.5 4.3 - - - +
1097B LEU* 2.7 78.1 + - + +
1098B LEU 4.7 4.3 - - - +
1103B LYS* 3.9 7.9 - - + +
1104B LYS* 1.3 76.5 - - - +
1106B HIS* 1.3 75.2 + - - +
1107B CYS* 5.2 0.2 - - + -
1143B LEU* 4.9 10.8 - - + -
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Residues in contact with HIS1106 (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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1306A GLU* 2.9 44.4 + - - +
1307A TYR* 5.9 1.7 - - - -
1079B HIS* 5.8 1.6 - + - -
1094B HIS* 2.7 36.0 + + + -
1095B GLY 3.5 14.8 - - - -
1096B THR* 4.8 2.9 - - - +
1104B LYS 4.4 0.2 - - - -
1105B ILE* 1.3 86.2 - - - +
1107B CYS* 1.3 69.7 + - - +
1143B LEU* 5.3 1.2 - - - +
1158B PRO* 5.6 0.2 - - - +
1159B TYR* 3.3 36.0 + + + +
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Residues in contact with CYS1107 (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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1076B LEU* 4.0 2.7 - - - -
1094B HIS* 3.6 4.5 - - - -
1095B GLY 2.8 48.8 + - - +
1096B THR 4.0 0.9 - - - -
1097B LEU* 4.0 20.4 - - + -
1105B ILE 4.4 0.7 - - - +
1106B HIS* 1.3 82.4 + - - +
1108B ALA* 1.3 57.6 + - - +
1109B VAL* 4.0 11.2 - - - -
1143B LEU* 4.1 14.1 - - + -
1156B VAL* 3.9 19.5 - - + -
1157B LEU 3.3 13.9 - - - +
1159B TYR* 4.3 13.5 - - - +
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Residues in contact with ALA1108 (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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2B IHX 3.5 42.2 - - + -
1084B ILE* 4.0 14.6 - - + -
1092B VAL* 4.1 2.5 - - + -
1093B TYR 3.3 5.6 - - - -
1107B CYS* 1.3 73.7 - - - +
1109B VAL* 1.3 63.3 + - - +
1155B VAL 3.8 0.2 - - - +
1156B VAL* 3.7 0.3 - - - -
1157B LEU* 2.8 39.4 + - - +
1158B PRO 4.2 2.7 - - - +
1159B TYR* 4.2 3.7 - - - +
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Residues in contact with VAL1109 (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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1076B LEU* 4.0 16.8 - - + -
1078B VAL* 3.9 28.3 - - + -
1091B CYS 3.7 1.4 - - - +
1092B VAL* 3.2 4.4 - - - -
1093B TYR* 2.7 45.4 + - + +
1095B GLY* 4.0 14.6 - - - -
1107B CYS* 4.0 20.4 - - - -
1108B ALA* 1.3 79.0 - - - +
1110B LYS* 1.3 62.5 + - - +
1154B LEU* 3.9 31.2 - - + -
1155B VAL 3.4 9.2 - - - +
1156B VAL* 4.6 4.0 - - + -
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Residues in contact with LYS1110 (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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1089B PHE* 4.3 3.0 - - - +
1090B GLY* 3.7 22.4 - - - +
1091B CYS 3.3 10.1 - - - +
1092B VAL* 4.1 14.1 - - + +
1108B ALA 4.2 0.4 - - - -
1109B VAL* 1.3 75.2 - - - +
1111B SER* 1.3 68.3 + - - +
1112B LEU* 3.8 17.5 + - + +
1154B LEU* 3.4 3.6 - - - -
1155B VAL* 2.7 50.2 + - + +
1157B LEU* 4.7 11.8 - - + +
1225B LEU 4.8 6.2 + - - +
1226B ALA* 4.1 4.6 + - - -
1227B ARG 4.0 6.7 + - - -
1228B ASP* 2.7 35.6 + - - +
1230B TYR* 3.0 29.2 + - - +
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Residues in contact with SER1111 (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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1080B PHE* 5.7 2.5 - - - -
1089B PHE 3.4 0.3 - - - +
1090B GLY* 3.2 26.2 - - - -
1091B CYS* 3.1 13.5 + - - -
1093B TYR* 4.5 14.1 - - - -
1109B VAL* 4.1 1.0 + - - +
1110B LYS* 1.3 75.4 - - - +
1112B LEU* 1.3 58.9 + - - +
1113B ASN* 3.0 29.3 + - - +
1148B ARG* 4.6 1.6 + - - -
1152B SER* 4.3 4.7 - - - -
1153B PRO 3.7 6.0 + - - -
1154B LEU* 3.8 17.8 - - - +
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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