Contacts of the strand formed by residues 112 - 116 (chain J) in PDB entry 5LN3
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 CYS 112 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75J GLU* 3.4 4.3 - - - -
76J VAL* 3.0 39.2 + - + +
108J VAL* 5.9 2.2 - - + -
109J THR 4.0 11.2 - - - +
110J PRO 3.5 0.4 - - - -
111J ASN* 1.4 79.3 - - - +
113J ARG* 1.3 78.9 + - - +
114J VAL* 3.8 2.2 + - + +
126J ILE* 4.1 22.9 - - + -
127J LEU 3.3 21.1 - - - -
128J PRO 3.6 8.5 - - - -
129J ASN* 4.2 7.6 - - - +
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Residues in contact with ARG 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J VAL* 4.8 6.5 - - + -
74J GLY 3.4 9.6 - - - +
75J GLU* 4.4 4.0 - - + +
90J HIS* 5.4 3.4 - - + -
111J ASN 4.2 0.8 + - - -
112J CYS* 1.3 80.4 - - - +
114J VAL* 1.4 54.8 + - - +
127J LEU* 2.8 54.1 + - + +
128J PRO* 3.2 49.8 + - - +
129J ASN* 3.3 17.4 + - - +
130J LYS* 3.9 32.8 - - + +
96K VAL* 5.9 1.0 - - - +
102K ILE* 4.1 24.0 - - - +
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Residues in contact with VAL 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J VAL* 3.6 9.4 - - - +
74J GLY 2.9 42.0 + - - +
75J GLU 4.2 0.7 - - - +
76J VAL* 3.9 24.0 - - + +
87J VAL* 4.6 1.1 - - + -
112J CYS* 4.2 4.0 - - + +
113J ARG* 1.4 77.2 - - - +
115J ALA* 1.4 71.9 + - - +
116J LEU* 3.8 14.6 - - + -
123J LEU* 3.4 31.6 - - + -
125J LYS 3.3 16.4 - - - +
126J ILE* 4.0 7.4 - - + -
127J LEU* 4.2 9.0 - - - +
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Residues in contact with ALA 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J SER* 4.5 10.1 - - - -
72J TYR 3.6 5.2 - - - -
73J VAL* 5.0 0.4 - - - +
114J VAL* 1.4 76.2 - - - +
116J LEU* 1.3 60.3 + - - +
123J LEU* 3.3 7.6 - - - -
124J HIS* 3.1 28.3 + - + -
125J LYS* 3.1 25.6 + - + +
127J LEU* 4.7 3.8 - - + +
112K TYR* 4.4 27.1 - - + -
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Residues in contact with LEU 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J SER* 3.5 5.4 - - - -
72J TYR* 3.1 39.5 + - + +
73J VAL 4.1 1.1 - - - -
74J GLY* 3.6 34.8 - - - +
87J VAL* 3.8 26.2 - - + -
89J VAL* 4.7 8.1 - - + -
97J VAL* 4.3 12.6 - - + -
114J VAL* 3.8 13.5 - - + -
115J ALA* 1.3 79.3 - - - +
117J ARG* 1.3 72.6 + - - +
118J ASN* 3.1 0.5 - - - +
121J TYR* 5.2 5.2 - - + -
122J THR 3.6 5.6 - - - +
123J LEU* 3.9 27.8 - - + -
124J HIS* 5.7 0.2 - - - -
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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