Contacts of the strand formed by residues 107 - 114 (chain B) in PDB entry 3NCF
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 LEU 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B PRO 4.5 4.7 - - - +
106B PRO* 1.3 77.3 - - - +
108B GLU* 1.3 77.4 + - + +
109B LEU* 3.3 4.0 + - - -
127B TRP* 3.6 3.3 - - - +
128B SER* 2.7 44.0 + - - +
129B PRO 3.8 9.0 - - - +
130B PRO* 4.3 4.5 - - + -
131B THR* 3.7 34.8 - - + +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 1.3 85.0 - - + +
109B LEU* 1.3 66.1 + - - +
110B ALA* 3.2 7.4 + - - +
126B LYS* 3.2 7.8 - - - +
127B TRP* 3.5 3.8 - - - -
128B SER* 2.8 28.5 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU 3.3 3.6 + - - -
108B GLU* 1.3 74.7 - - - +
110B ALA* 1.3 60.0 + - - +
111B VAL* 4.6 1.3 - - + -
125B ILE* 3.5 32.1 - - + -
126B LYS 3.2 8.3 - - - +
127B TRP* 4.2 9.6 - - + -
146B ILE* 5.8 0.2 - - + -
180B VAL* 3.5 31.4 - - + +
181B GLN* 4.0 7.6 - - - -
182B VAL* 4.3 18.4 - - + +
195B SER* 3.8 21.1 - - - +
196B PRO 4.1 3.1 - - - +
198B THR* 3.2 38.1 - - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLU 3.2 4.4 + - - +
109B LEU* 1.3 75.6 - - - +
111B VAL* 1.3 69.9 + - - +
112B GLU* 6.4 0.4 - - + -
124B TRP 3.6 0.9 - - - +
125B ILE* 3.4 1.2 - - - +
126B LYS* 2.7 56.7 + - + +
198B THR* 4.9 0.9 - - - -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.6 2.2 - - + -
110B ALA* 1.3 84.3 - - - +
112B GLU* 1.3 69.5 + - - +
123B LEU* 3.2 45.1 - - + -
124B TRP 3.3 6.1 - - - +
125B ILE* 4.4 14.1 - - + -
180B VAL* 4.3 15.9 - - + -
198B THR* 3.3 23.9 + - - +
199B PHE 5.8 0.7 - - - +
200B ILE* 4.1 25.2 - - + +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 6.4 0.7 - - + -
111B VAL* 1.3 82.5 - - - +
113B VAL* 1.3 66.8 + - - +
114B LYS* 3.6 12.7 + - + +
123B LEU* 3.3 8.1 - - - +
124B TRP* 3.0 54.5 + - + +
126B LYS* 5.9 1.8 - - - -
200B ILE* 4.9 4.0 - - - -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 1.3 78.4 - - - +
114B LYS* 1.3 66.1 + - - +
115B GLN* 3.9 23.6 + - + +
122B TYR 3.7 2.5 - - - +
123B LEU* 4.1 14.4 - - + -
200B ILE* 4.2 9.7 - - + +
201B GLN 4.1 10.8 - - - +
202B ILE* 4.2 9.6 - - + -
203B PRO* 3.9 27.4 - - + -
206B PHE* 3.8 26.2 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 3.6 13.8 + - - +
113B VAL* 1.3 76.9 - - - +
115B GLN* 1.3 62.9 + - - +
116B PRO* 3.6 4.1 - - + +
121B PRO* 3.3 4.2 - - - +
122B TYR* 2.7 85.6 + - + +
124B TRP* 4.2 24.8 - - + +
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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