Contacts of the strand formed by residues 1108 - 1113 (chain B) in PDB entry 1Y8Z
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 ARG1108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B ASP 3.0 14.0 + - - +
1077B ILE* 3.4 16.5 - - + +
1078B LEU 2.8 27.5 + - - +
1106B SER 3.4 4.2 + - - +
1107B ILE* 1.3 71.2 - - - +
1109B VAL* 1.3 61.1 + - - +
1110B VAL* 4.4 11.2 - - + -
1135B ASP* 3.3 18.1 - - + +
1136B VAL* 4.7 5.8 - - + -
1398B ILE* 2.8 45.4 + - + +
1399B THR* 3.0 24.8 + - - +
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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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1078B LEU* 3.4 10.5 - - + +
1080B ILE* 3.9 28.5 - - + -
1100B LEU* 5.4 0.2 - - + -
1103B ILE* 3.5 20.6 - - + -
1107B ILE* 3.9 5.2 - - + +
1108B ARG* 1.3 73.7 - - - +
1110B VAL* 1.3 62.2 + - - +
1111B VAL* 4.2 5.4 - - + -
1130B THR 5.3 0.4 - - - +
1133B ARG* 3.3 44.9 - - + +
1134B ALA* 3.7 14.9 - - - +
1135B ASP* 2.7 38.3 + - - +
1136B VAL 3.1 6.9 + - - +
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Residues in contact with VAL1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B ILE* 4.1 14.4 - - + -
1078B LEU 2.8 11.4 + - - +
1079B ILE* 3.3 9.7 - - + +
1080B ILE* 2.8 27.2 + - - +
1108B ARG* 4.4 4.0 - - + -
1109B VAL* 1.3 78.1 - - - +
1111B VAL* 1.3 63.8 + - - +
1112B TYR* 3.6 19.5 - - + -
1136B VAL* 3.4 16.2 - - + +
1138B PHE* 3.6 32.1 - - + -
1398B ILE* 3.9 32.8 - - + -
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Residues in contact with VAL1111 (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 ILE* 3.5 13.0 - - + +
1083B VAL* 6.1 0.9 - - + -
1109B VAL* 4.2 10.3 - - + -
1110B VAL* 1.3 75.9 - - - +
1112B TYR* 1.3 70.9 + - - +
1113B GLN* 4.8 4.7 - - + +
1127B LEU* 5.5 7.2 - - + -
1130B THR* 3.6 33.9 - - + +
1131B VAL* 5.8 2.5 - - + +
1134B ALA* 3.3 28.7 - - + -
1136B VAL 2.8 12.6 + - - +
1137B ILE* 3.3 14.0 - - + +
1138B PHE* 2.9 26.9 + - - +
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Residues in contact with TYR1112 (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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1019B PHE* 3.6 12.6 - + - -
1023B GLN* 3.3 22.6 + - - -
1079B ILE* 3.5 12.1 - - + -
1080B ILE 3.1 10.0 + - - +
1081B ASN* 3.2 35.3 - - - +
1110B VAL* 3.6 22.0 - - + -
1111B VAL* 1.3 75.9 - - - +
1113B GLN* 1.3 60.5 + - - +
1114B HIS* 3.4 19.1 + - + +
1138B PHE* 3.5 35.3 - + + -
1174B PHE* 3.8 16.8 - + + -
1391B PHE* 5.0 0.5 - - - -
1394B GLN* 2.6 44.3 + - - +
1398B ILE* 3.9 8.1 - - + +
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Residues in contact with GLN1113 (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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1111B VAL* 4.0 5.2 + - + +
1112B TYR* 1.3 71.9 - - - +
1114B HIS* 1.3 64.7 + - - +
1115B ASP* 2.9 54.8 + - - +
1121B LEU* 3.5 23.3 - - + +
1124B ASN* 4.5 2.9 + - - +
1127B LEU* 3.9 23.0 - - - +
1137B ILE* 5.5 5.2 - - + -
1138B PHE 2.9 19.3 + - - +
1139B SER* 3.7 15.1 - - - -
1140B HIS* 3.8 4.2 + - - -
1174B PHE* 3.6 15.8 - - - -
5004B GOL 6.2 0.2 - - - +
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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