Contacts of the strand formed by residues 113 - 117 (chain C) in PDB entry 5T0I
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 ARG 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C VAL* 3.9 9.6 - - + -
75C GLU* 3.4 26.1 + - - +
90C HIS* 6.0 0.2 + - - -
112C CYS* 1.3 77.1 - - - +
114C VAL* 1.3 67.0 + - - +
127C LEU* 2.9 44.3 + - + +
128C PRO 2.6 30.9 + - - -
129C ASN* 3.0 32.6 + - + +
130C LYS* 3.6 24.7 + - - +
93D LEU* 3.8 20.9 - - - +
94D GLU* 2.9 14.2 + - - -
102D ILE* 3.7 26.2 - - - -
110D ASN* 5.2 1.4 - - - +
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Residues in contact with VAL 114 (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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73C VAL* 3.2 4.3 - - - +
74C GLY* 2.7 53.8 + - - +
75C GLU 4.1 2.0 - - - +
76C VAL* 4.3 16.4 - - + +
87C VAL* 5.5 1.3 - - + -
108C VAL* 5.1 4.0 - - + -
112C CYS 4.2 8.7 - - - +
113C ARG* 1.3 81.1 - - - +
115C ALA* 1.3 55.4 + - - +
123C LEU* 3.7 41.3 - - + -
125C LYS 4.1 7.4 - - - +
126C ILE* 3.7 22.0 - - + -
127C LEU* 3.8 9.0 - - - -
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Residues in contact with ALA 115 (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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72C TYR 3.8 3.6 - - - -
73C VAL* 4.2 2.2 - - - +
114C VAL* 1.3 74.7 - - - +
116C LEU* 1.3 59.1 + - - +
123C LEU* 3.1 32.1 - - - +
124C HIS* 4.2 4.3 - - + +
125C LYS 3.7 24.2 + - - +
127C LEU* 3.7 11.5 - - + +
112D TYR* 3.4 42.8 - - + -
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Residues in contact with LEU 116 (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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71C SER* 3.3 5.6 - - - -
72C TYR* 2.5 79.0 + - + +
73C VAL 3.8 1.1 - - - +
74C GLY 3.9 6.3 - - - +
87C VAL* 3.7 34.8 - - + -
89C VAL* 4.4 12.1 - - + -
95C PHE* 4.7 5.6 - - + -
115C ALA* 1.3 76.1 - - - +
117C ARG* 1.3 64.9 + - - +
121C TYR* 3.3 40.4 - - + +
122C THR 3.2 9.9 - - - +
123C LEU* 4.1 1.8 - - + -
124C HIS* 5.3 0.4 - - - -
112D TYR* 4.9 2.2 - - - +
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Residues in contact with ARG 117 (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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62C GLU* 4.8 5.9 + - - -
65C LEU* 3.7 41.4 + - - +
71C SER* 4.2 11.1 + - - +
72C TYR 4.7 0.8 + - - -
102C ASN* 6.1 1.1 - - - +
116C LEU* 1.3 76.9 - - - +
118C ASN* 1.3 62.0 + - - +
119C ASP* 3.7 24.0 + - - +
120C SER* 4.3 3.8 + - - -
121C TYR* 3.1 29.6 - - - +
122C THR* 2.8 40.7 + - - +
124C HIS* 3.8 50.6 + - + +
112D TYR* 6.3 0.4 - - + -
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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