Contacts of the strand formed by residues 106 - 112 (chain D) in PDB entry 1N13
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 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D PYR 3.6 15.5 - - - +
54D ILE* 3.9 14.6 - - + -
94D SER 3.8 0.3 - - - +
95D VAL* 3.2 2.9 - - - -
96D ALA* 2.8 36.4 + - + +
105D GLY* 1.3 73.0 - - - -
107D ILE* 1.3 61.0 + - - +
108D MET* 3.9 17.8 + - + -
127D ALA* 3.8 12.7 - - - +
130D GLY* 3.3 37.0 - - - -
131D PHE* 3.7 17.6 - - + +
134D ARG* 3.5 20.2 - - - +
136D TRP* 6.1 0.4 - - + -
7015D AG2 3.9 23.6 - - + -
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.4 7.9 - - + -
53D PYR 2.8 36.5 + - + +
54D ILE 4.1 10.5 - - - +
55D MET* 4.1 7.6 - - - +
76D ALA* 3.9 11.4 - - + -
93D ILE* 3.8 13.5 - - + -
94D SER 3.2 10.1 - - - +
95D VAL* 4.1 17.3 - - + -
106D LEU* 1.3 75.7 - - - +
108D MET* 1.3 65.5 + - - +
109D GLU* 4.7 0.2 - - - +
160D ALA* 3.6 34.5 - - + -
162D LEU* 4.1 20.2 - - + -
7015D AG2 3.0 28.5 + - - +
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Residues in contact with MET 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 3.3 7.6 - - - +
94D SER* 2.9 44.6 + - - +
106D LEU* 3.9 16.1 + - + -
107D ILE* 1.3 77.2 - - - +
109D GLU* 1.3 63.6 + - - +
123D VAL* 3.3 11.7 - - + +
126D MET* 3.8 10.8 - - + +
127D ALA* 3.7 23.8 - - + +
7015D AG2 4.0 14.4 - - + -
31E LEU* 3.5 29.4 - - - +
32E ASN* 3.4 26.2 - - - +
35E ASP* 3.9 24.5 - - + +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 4.6 7.6 + - - +
51C ILE 5.0 5.0 - - - +
52C SER* 5.9 1.2 - - - -
76D ALA* 4.2 9.5 - - - +
77D TYR 3.5 26.7 + - - +
78D GLY* 3.9 17.7 - - - +
92D ALA 3.4 6.1 - - - +
93D ILE* 3.8 13.5 - - + -
107D ILE 4.2 0.2 - - - +
108D MET* 1.3 77.7 - - - +
110D TYR* 1.3 62.9 - - - +
111D GLU* 4.7 3.3 - - - +
123D VAL* 3.9 2.5 - - - -
126D MET* 3.6 17.2 - - - +
7015D AG2 2.7 32.1 + - - -
31E LEU* 3.6 18.5 - - + +
7005F MRD 4.5 10.1 + - + +
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Residues in contact with TYR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLY* 4.7 1.6 - - - -
91D ALA* 3.2 3.8 - - - +
92D ALA* 2.8 32.8 + - + +
109D GLU* 1.3 77.5 - - - +
111D GLU* 1.3 98.6 + - - +
112D GLY* 4.5 4.0 - - - -
114D CYS* 3.9 27.9 - - - +
118D GLU* 4.7 6.9 + - - -
119D ALA* 3.8 26.5 - - + +
122D THR* 3.7 30.1 + - + +
123D VAL* 3.9 19.1 - - + -
126D MET* 4.1 11.7 - - + -
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 5.3 2.7 + - - -
78D GLY* 3.2 25.5 - - - -
79D TYR* 3.2 35.7 - - - +
80D ILE* 4.0 6.1 - - + -
90D SER 3.2 11.9 - - - +
91D ALA* 4.4 1.1 - - - -
109D GLU* 4.7 3.5 - - - +
110D TYR* 1.3 101.2 + - - +
112D GLY* 1.3 60.3 + - - +
7005F MRD 6.0 1.7 - - - +
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Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 3.5 16.4 - - - +
89D ILE* 3.6 1.7 - - - -
90D SER* 2.9 33.1 + - - +
110D TYR* 4.3 11.1 - - - -
111D GLU* 1.3 75.7 - - - +
113D LYS* 1.3 61.4 + - - -
114D CYS* 3.1 7.5 + - - -
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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