Contacts of the strand formed by residues 99 - 106 (chain C) in PDB entry 5IYB
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 VAL 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.5 6.5 - - + -
82C LEU* 4.5 18.6 - - + -
98C SER* 1.3 77.3 - - - +
100C GLU* 1.3 68.0 + - - +
101C PHE* 4.0 13.5 - - + -
122C SER* 4.6 2.5 - - - -
124C SER* 3.2 27.4 - - - +
128C ILE* 3.7 33.4 - - + -
164C TYR* 3.4 9.5 - - - -
165C ALA* 2.8 40.4 + - + +
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Residues in contact with GLU 100 (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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99C VAL* 1.3 76.6 - - - +
101C PHE* 1.3 72.7 + - - +
102C THR* 5.4 3.5 - - - -
122C SER* 3.4 7.4 - - - -
123C ASN* 3.0 56.1 + - + +
124C SER* 3.3 7.4 + - - +
162C ARG* 3.4 25.9 + - - +
163C ALA 3.7 2.5 - - - +
164C TYR* 3.4 35.6 + - + -
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Residues in contact with PHE 101 (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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47C ILE* 4.5 9.2 - - + -
73C LEU* 3.9 33.9 - - + -
99C VAL* 4.0 12.6 - - + -
100C GLU* 1.3 82.0 - - - +
102C THR* 1.3 62.1 + - - +
120C LEU* 3.8 28.0 - - + -
121C ILE 3.4 17.9 - - - -
122C SER* 3.7 18.2 - - - -
128C ILE 3.5 22.7 - - - -
129C PRO* 4.6 1.1 - - + -
130C VAL* 4.2 20.2 - - + -
162C ARG* 3.8 3.1 - - - +
163C ALA* 2.7 46.5 + - + +
165C ALA* 4.0 17.5 - - + -
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Residues in contact with THR 102 (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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100C GLU* 5.4 4.9 - - - -
101C PHE* 1.3 76.5 - - - +
103C LEU* 1.3 64.9 + - - +
104C ASP* 5.6 1.6 - - - +
119C ASP 4.2 1.2 - - - +
120C LEU* 3.6 4.3 - - - +
121C ILE* 3.0 57.3 + - + +
123C ASN* 5.2 9.6 - - + +
161C LEU* 3.8 9.8 + - - -
162C ARG* 4.5 9.2 - - - +
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Residues in contact with LEU 103 (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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68C LEU* 5.4 2.9 - - + -
102C THR* 1.3 79.1 + - - +
104C ASP* 1.3 66.3 + - - +
105C VAL* 4.0 20.4 - - + -
115C VAL* 4.0 22.2 - - + -
116C THR 5.3 0.2 - - - +
119C ASP* 3.8 31.6 - - + +
120C LEU* 4.0 13.5 - - + +
150C ILE* 4.8 12.1 - - + -
159C LEU* 4.1 24.5 - - + +
160C ARG* 3.4 5.4 - - - +
161C LEU* 3.1 53.6 + - + +
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Residues in contact with ASP 104 (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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102C THR* 4.4 2.2 - - - +
103C LEU* 1.3 78.6 - - - +
105C VAL* 1.3 71.0 + - - +
106C ARG* 3.3 27.0 + - - -
119C ASP 5.2 1.6 + - - +
159C LEU 3.5 2.0 - - - +
160C ARG* 3.1 51.9 + - + +
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Residues in contact with VAL 105 (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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103C LEU* 4.0 17.7 - - + -
104C ASP* 1.3 82.7 + - - +
106C ARG* 1.3 68.7 + - - +
113C ARG* 4.3 24.0 - - - +
115C VAL* 4.2 21.8 - - + -
119C ASP* 4.1 17.9 - - + -
153C LEU* 3.9 20.9 - - + -
158C GLU* 3.6 2.8 - - - +
159C LEU* 3.1 41.3 + - + +
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Residues in contact with ARG 106 (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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104C ASP* 3.3 39.1 + - - -
105C VAL* 1.3 78.2 + - - +
107C CYS* 1.3 60.0 + - - +
108C ASN* 3.5 16.2 + - + +
109C GLU* 4.8 1.0 - - - +
113C ARG* 4.2 19.6 + - - +
153C LEU* 4.8 3.4 - - - -
156C GLY 6.3 0.2 - - - -
157C GLN 3.8 7.2 - - - +
158C GLU* 3.4 33.7 + - + +
160C ARG* 3.6 14.1 - - - +
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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