Contacts of the strand formed by residues 113 - 123 (chain B) in PDB entry 4N6N
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 SER 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B LEU 4.6 0.2 - - - -
107B VAL* 3.6 8.0 - - - +
108B VAL* 3.1 48.2 + - - +
111B GLN* 3.8 14.8 + - - +
112B ASN* 1.3 77.7 - - - +
114B SER* 1.3 63.3 + - - +
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Residues in contact with SER 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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29B ALA* 3.4 33.2 + - - +
105B VAL* 4.4 5.8 - - - -
106B LEU 3.3 8.7 - - - -
107B VAL* 4.7 6.3 - - - -
113B SER* 1.3 76.2 - - - +
115B GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 115 (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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105B VAL* 3.4 4.1 - - - +
106B LEU* 2.8 56.3 + - + +
114B SER* 1.3 78.2 - - - +
116B LEU* 1.3 65.5 + - - +
117B LEU* 3.1 31.9 + - + +
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Residues in contact with LEU 116 (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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29B ALA 5.3 0.2 - - - +
30B ALA* 3.7 13.5 - - + +
33B SER* 3.4 26.1 + - - +
34B TYR* 3.6 36.3 - - + +
103B PHE* 3.8 26.5 - - + -
104B GLU 3.7 9.0 - - - +
105B VAL* 4.1 12.7 - - + +
115B GLN* 1.3 73.6 - - - +
117B LEU* 1.3 60.5 + - - +
118B LYS 3.4 26.9 - - - +
119B HIS* 4.4 15.0 - - + -
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Residues in contact with LEU 117 (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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61B LYS* 3.7 35.0 - - + +
104B GLU* 2.8 19.5 + - + +
106B LEU* 3.8 24.5 - - + +
115B GLN* 3.7 39.0 - - + +
116B LEU* 1.3 73.8 - - - +
118B LYS* 1.3 69.0 + - + +
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Residues in contact with LYS 118 (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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102B ASP 4.4 1.3 - - - -
103B PHE* 3.4 1.0 - - - -
104B GLU* 2.9 58.9 + - + +
116B LEU* 3.4 11.1 - - - +
117B LEU* 1.3 89.7 - - + +
119B HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 119 (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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217A TYR* 3.4 50.6 + + - +
264A THR* 4.4 17.4 - - + +
34B TYR* 4.0 17.6 - + + -
102B ASP 3.3 6.1 - - - -
103B PHE* 3.6 26.2 - - + -
116B LEU* 4.4 14.6 - - + -
117B LEU 6.2 0.2 - - - -
118B LYS* 1.3 79.5 - - - +
120B ASN* 1.3 64.0 + - - +
121B CYS* 4.8 2.4 + - - -
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ARG 3.8 2.3 - - - +
101B CYS* 3.5 1.4 - - - -
102B ASP* 2.9 50.3 + - + +
119B HIS* 1.3 75.1 - - - +
121B CYS* 1.3 64.3 + - - +
122B VAL* 4.2 2.6 + - - +
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Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A GLU* 5.8 4.3 - - - +
217A TYR* 4.3 7.1 + - - +
34B TYR* 3.5 39.9 - - + +
99B LEU* 4.3 7.2 - - + -
100B ARG 3.5 3.1 - - - -
101B CYS* 2.0 46.7 - - - -
103B PHE* 3.9 9.2 - - - -
119B HIS* 4.1 3.9 + - - -
120B ASN* 1.3 80.7 + - - +
122B VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 122 (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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214A GLU* 6.6 0.4 - - - -
99B LEU* 3.5 4.4 - - - -
100B ARG* 3.0 44.2 + - + +
120B ASN* 5.5 2.9 - - - +
121B CYS* 1.3 75.6 - - - +
123B GLN* 1.3 72.7 + - - +
124B MET* 3.4 1.9 + - + +
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Residues in contact with GLN 123 (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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190A GLU* 3.8 3.0 + - - -
213A ARG* 2.9 72.4 + - + +
214A GLU* 6.2 0.4 - - - +
96B GLN 5.3 1.4 - - - +
97B GLU* 3.3 39.1 + - + +
98B LYS 3.5 13.2 + - - +
99B LEU* 3.6 10.3 - - + +
122B VAL* 1.3 84.1 - - - +
124B MET* 1.3 72.8 + - - +
125B LEU* 3.7 2.9 + - - +
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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