Contacts of the strand formed by residues 1110 - 1116 (chain C) in PDB entry 5YS0
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 ALA1110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106C PHE* 3.3 9.9 - - - +
1107C VAL* 3.0 29.8 - - - +
1108C ASN 2.8 10.4 + - - +
1109C ASN* 1.3 81.0 - - - +
1111C ARG* 1.3 59.5 + - - +
1133C THR* 5.8 2.0 - - + -
1134C GLU 3.8 3.8 - - - -
1135C THR* 3.7 22.7 - - + -
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Residues in contact with ARG1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080C LEU 2.9 28.1 + - - -
1081C TYR* 3.5 16.4 + - - +
1082C GLY 4.0 3.0 + - - -
1085C THR* 4.0 19.2 - - - +
1088C ILE* 3.7 20.0 - - - +
1103C ILE* 5.0 3.0 + - - +
1104C PRO* 3.1 40.3 + - + +
1105C LYS* 4.1 4.2 - - - +
1106C PHE* 3.2 31.6 - - + -
1107C VAL* 4.4 5.2 - - - -
1110C ALA* 1.3 75.4 - - - +
1112C GLU* 1.3 59.4 + - - +
1113C ILE* 3.3 26.3 - - + +
1133C THR* 4.0 4.2 - - - +
1134C GLU* 2.4 55.3 + - - +
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Residues in contact with GLU1112 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101C CYS* 4.9 2.9 - - - -
1104C PRO* 3.5 25.9 - - + +
1107C VAL* 5.5 0.6 - - - +
1111C ARG* 1.3 72.7 - - - +
1113C ILE* 1.3 66.2 + - - +
1114C THR* 5.0 4.3 + - - +
1131C ILE* 4.0 21.9 - - + +
1132C VAL 3.5 13.7 - - - +
1133C THR* 3.4 17.7 + - + +
1152C ARG* 5.2 2.6 + - - -
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Residues in contact with ILE1113 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1092C ILE* 4.6 10.3 - - + -
1100C VAL* 6.5 0.2 - - - -
1101C CYS* 4.7 2.9 - - - -
1103C ILE* 3.4 39.9 - - + -
1111C ARG* 3.3 49.4 - - + +
1112C GLU* 1.3 76.5 - - - +
1114C THR* 1.3 69.5 + - - +
1115C TYR* 3.3 26.6 - - + -
1130C CYS 3.4 0.2 - - - +
1132C VAL* 3.0 48.4 + - + +
1134C GLU* 4.8 8.1 - - - +
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Residues in contact with THR1114 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1099C ASN 3.2 2.4 - - - +
1101C CYS* 3.0 41.6 + - + +
1112C GLU* 5.0 5.5 + - - +
1113C ILE* 1.3 83.7 + - - +
1115C TYR* 1.3 74.5 + - - +
1129C LYS* 5.8 4.5 - - + -
1130C CYS 3.3 17.1 + - - +
1131C ILE* 4.3 12.2 - - + +
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Residues in contact with TYR1115 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1092C ILE* 4.6 11.8 - - + +
1097C ASN* 3.1 33.0 - - + -
1098C PHE 3.2 12.6 - - - +
1099C ASN* 3.3 14.8 - - - +
1100C VAL* 3.9 17.5 - - + -
1113C ILE* 3.3 31.0 - - + -
1114C THR* 1.3 87.1 - - - +
1116C THR* 1.3 71.8 + - - +
1129C LYS* 3.6 1.0 - - - +
1130C CYS* 3.1 47.2 + - + +
1132C VAL* 3.3 32.4 - - + +
1149C GLN* 5.8 0.3 + - - -
1151C VAL* 5.4 1.7 - - - +
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Residues in contact with THR1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C ASN* 3.0 21.4 - - - +
1098C PHE* 3.0 12.5 + - - +
1099C ASN* 3.4 34.8 + - + +
1114C THR* 6.3 0.2 - - + -
1115C TYR* 1.3 84.6 - - - +
1117C LYS* 1.3 62.2 + - - +
1127C GLN* 3.9 18.2 - - + +
1128C THR 3.1 28.5 + - - -
1129C LYS* 4.0 21.5 - - + -
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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