Contacts of the strand formed by residues 112 - 116 (chain C) in PDB entry 1L9W
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 MET 112 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 4.2 18.2 - - + -
11C ILE* 4.6 11.9 - - + -
44C ILE* 3.7 33.9 - - + -
76C PRO* 3.9 24.9 - - + -
77C LEU 3.1 5.8 + - - +
78C LEU* 3.5 22.5 - - + -
79C PHE* 2.8 26.5 + - - +
110C VAL* 3.5 2.7 - - - +
111C ASP* 1.4 85.7 - - + +
113C ILE* 1.3 66.2 - - - +
136C VAL* 3.9 1.3 - - - -
137C TYR* 3.3 26.2 - - + +
139C VAL* 4.6 15.7 - - + -
168C ILE* 5.0 4.5 - - - -
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Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.7 4.9 - - - +
79C PHE* 3.2 19.7 - - + +
101C ASN* 3.7 24.5 - - + +
104C ALA* 4.6 0.4 - - + -
105C ILE* 4.0 31.9 - - + -
110C VAL* 4.2 6.7 - - + -
112C MET* 1.3 80.3 - - - +
114C ASP* 1.3 62.7 + - - +
115C LEU* 3.9 25.8 - - + -
127C THR* 4.5 4.9 - - + -
131C ALA* 4.5 1.8 - - + -
136C VAL* 4.1 13.7 - - + -
137C TYR 3.1 9.5 + - - +
138C VAL* 4.1 17.9 - - + -
139C VAL* 3.0 24.8 + - - +
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 4.9 1.4 - - - +
78C LEU* 4.5 4.7 - - + +
79C PHE 2.9 8.9 + - - +
80C THR* 3.3 27.5 + - + +
81C PHE 5.1 4.6 + - - +
82C ARG* 3.1 34.6 + - - -
97C TYR* 3.8 7.3 + - - -
101C ASN* 4.1 8.5 + - - +
113C ILE* 1.3 76.4 - - - +
115C LEU* 1.3 73.4 + - - +
116C GLU* 4.2 0.3 - - - +
139C VAL* 3.2 18.8 - - + +
141C SER* 2.8 30.1 + - - -
170C LYS* 4.5 3.6 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TYR* 3.4 15.9 - - + +
98C LEU* 5.3 2.5 - - + -
101C ASN* 4.2 12.6 - - + +
113C ILE* 3.9 18.8 + - + -
114C ASP* 1.3 85.2 + - - +
116C GLU* 1.3 60.1 + - - +
124C VAL* 3.8 38.4 - - + +
127C THR* 3.9 26.0 - - + -
128C VAL* 3.9 18.2 - - + +
138C VAL* 4.1 16.8 - - + -
139C VAL 2.9 7.3 + - - -
140C MET* 3.3 10.1 - - + +
141C SER 3.0 19.4 + - - -
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Residues in contact with GLU 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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81C PHE 3.7 1.6 - - - +
82C ARG* 2.9 35.7 + - - +
83C SER* 2.8 50.6 + - - -
85C LYS* 4.5 5.9 - - - +
86C GLU* 3.9 27.1 - - - +
97C TYR* 2.9 20.8 + - - +
115C LEU* 1.3 71.2 - - - +
117C LEU* 1.3 63.7 + - - +
118C PHE 3.2 1.1 - - - +
119C THR* 2.8 32.1 + - - +
124C VAL* 3.6 6.5 - - - +
141C SER* 3.3 12.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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