Contacts of the strand formed by residues 109 - 114 (chain H) in PDB entry 1IBL
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 ILE 109 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152E ARG* 4.6 4.3 - - - +
38H ILE* 4.0 4.5 - - + -
39H LEU* 4.8 0.7 - - + -
42H GLU* 3.9 35.0 - - + +
44H PHE* 3.6 29.6 - - + -
103H VAL* 2.8 18.3 - - - +
108H GLY* 1.3 82.2 - - - +
110H ALA* 1.3 63.8 + - - +
111H ILE* 3.9 26.0 - - + -
120H THR* 4.8 7.6 - - + -
121H ASP* 3.7 9.6 - - - +
136H GLU* 3.5 0.2 - - - -
137H VAL* 2.9 44.6 + - + +
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H PRO* 4.4 17.5 - - + -
103H VAL* 3.5 15.3 - - + -
109H ILE* 1.3 80.1 - - - +
111H ILE* 1.3 63.5 + - - +
112H LEU* 3.1 10.6 - - + +
120H THR* 4.4 1.1 - - - -
121H ASP* 3.0 39.7 + - + +
133H LEU* 5.3 5.2 - - + -
135H CYS 3.2 12.8 - - - +
136H GLU* 4.7 1.8 - - + -
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Residues in contact with ILE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LEU* 6.4 0.2 - - + -
35H ILE* 3.5 31.2 - - + -
38H ILE* 3.8 34.1 - - + -
39H LEU* 4.1 20.0 - - + -
109H ILE* 3.9 11.2 - - + -
110H ALA* 1.3 72.8 - - - +
112H LEU* 1.3 62.1 + - - +
118H VAL* 3.7 26.7 - - + -
119H LEU 3.8 5.2 - - - +
120H THR* 4.5 1.1 - - - +
133H LEU* 4.1 1.0 - - - +
134H ILE* 3.0 29.2 + - + +
135H CYS* 3.1 30.8 + - - +
137H VAL* 4.6 1.8 - - + -
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H VAL* 4.5 9.4 - - + -
100H ILE* 4.1 32.8 - - + -
101H PRO* 5.7 0.4 - - + -
110H ALA* 3.1 19.1 - - + +
111H ILE* 1.3 73.9 - - - +
113H SER* 1.3 63.0 + - - +
114H THR* 3.8 5.4 + - + +
117H GLY 3.8 0.7 - - - +
118H VAL* 3.5 0.8 - - - -
119H LEU 3.0 41.7 + - - +
120H THR 3.7 11.2 - - - +
121H ASP* 3.9 7.0 - - + +
124H ALA* 4.3 8.1 - - + -
130H GLY* 4.7 1.3 - - - -
131H GLY 4.4 17.9 - - - +
132H GLU 3.4 15.7 - - - +
133H LEU* 3.7 11.4 - - + -
134H ILE* 3.7 6.1 - - - +
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Residues in contact with SER 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A A 2.6 49.7 + - - +
643A C 3.5 10.1 + - - -
31H PHE* 4.3 1.8 - - - -
112H LEU* 1.3 72.1 - - - +
114H THR* 1.3 57.4 + - - +
117H GLY 3.7 3.4 - - - -
118H VAL* 4.0 7.5 - - - +
131H GLY* 3.5 2.4 - - - -
132H GLU* 3.1 34.2 + - - -
134H ILE* 3.6 22.1 - - - +
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Residues in contact with THR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A A 2.7 29.9 - - - -
112H LEU* 4.2 15.7 - - + +
113H SER* 1.3 77.0 + - - +
115H SER* 1.3 52.5 + - - +
116H LYS* 2.9 16.4 + - - +
117H GLY 2.6 44.6 + - - +
119H LEU* 3.4 10.9 - - + +
124H ALA* 4.9 0.7 - - + -
129H VAL* 3.9 17.2 - - + +
130H GLY* 3.0 35.7 - - - +
131H GLY* 4.1 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