Contacts of the strand formed by residues 106 - 112 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53H PYR 3.6 15.3 - - - +
54H ILE* 4.0 6.5 - - + -
94H SER 3.8 0.5 - - - +
95H VAL* 3.3 3.3 - - - -
96H ALA* 2.8 36.5 + - + +
105H GLY* 1.3 72.8 - - - -
107H ILE* 1.3 66.6 + - - +
108H MET* 3.9 21.9 + - + -
127H ALA* 3.7 15.8 - - - +
130H GLY* 3.3 35.9 - - - -
131H PHE* 3.7 17.6 - - + +
134H ARG* 3.7 30.1 - - - +
136H TRP* 6.2 0.4 - - + -
7012H AG2 4.9 3.8 - - + -
35K ASP* 4.1 7.9 - - - +
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Residues in contact with ILE 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G VAL* 4.6 3.4 - - + -
51G ILE* 4.8 0.7 - - + -
53H PYR 2.8 27.2 + - + +
54H ILE 4.0 23.6 - - - +
55H MET* 4.1 9.6 - - + +
76H ALA* 3.8 13.2 - - + -
93H ILE* 3.8 14.1 - - + -
94H SER 3.3 10.5 - - - +
95H VAL* 4.1 16.2 - - + -
106H LEU* 1.3 76.7 - - - +
108H MET* 1.3 61.0 + - - +
160H ALA* 3.7 29.6 - - + -
162H LEU* 4.1 22.9 - - + -
7012H AG2 2.7 29.2 + - - +
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H ILE* 3.4 7.3 - - - +
94H SER* 2.9 44.5 + - - +
106H LEU* 3.9 20.2 + - + -
107H ILE* 1.3 75.6 - - - +
109H GLU* 1.3 61.5 + - - +
123H VAL* 3.3 11.6 - - + +
126H MET* 3.8 13.2 - - + +
127H ALA* 3.7 24.9 - - + +
7012H AG2 4.0 6.5 - - + -
31K LEU* 3.6 29.8 - - + +
32K ASN* 3.7 21.8 - - - +
35K ASP* 3.9 31.2 - - + +
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ARG* 4.6 6.9 + - - +
51G ILE 5.0 5.0 - - - +
52G SER* 5.8 1.0 - - - -
76H ALA* 4.2 10.5 - - - +
77H TYR 3.6 25.3 + - - +
78H GLY* 3.9 19.7 - - - +
92H ALA 3.4 7.2 - - - +
93H ILE* 3.9 9.6 - - + -
108H MET* 1.3 76.2 + - - +
110H TYR* 1.3 63.0 + - - +
111H GLU* 4.6 4.0 - - - +
123H VAL* 3.8 2.2 - - - -
126H MET* 3.5 8.3 - - - +
7012H AG2 2.6 38.7 + - - -
31K LEU* 3.3 24.1 - - + +
7002L MRD 4.3 15.8 + - + +
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H GLY* 5.0 1.7 - - - -
91H ALA* 3.3 3.6 - - - +
92H ALA* 2.8 33.0 + - + +
109H GLU* 1.3 76.8 - - - +
111H GLU* 1.3 91.4 + - - +
112H GLY* 4.5 3.8 - - - -
114H CYS* 4.0 18.0 - - - +
119H ALA* 3.8 35.0 - - + +
122H THR* 3.7 30.3 + - + -
123H VAL* 3.9 19.1 - - + -
126H MET* 4.0 13.9 - - + -
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Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ARG* 5.5 1.8 + - - -
78H GLY* 3.5 18.9 - - - -
79H TYR* 3.3 37.0 - - - +
80H ILE* 3.9 7.0 - - + -
90H SER 3.2 12.6 - - - +
91H ALA* 4.5 1.3 - - - -
109H GLU* 4.6 4.3 - - - +
110H TYR* 1.3 103.9 + - - +
112H GLY* 1.3 58.9 + - - +
7002L MRD 5.8 4.3 - - - +
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Residues in contact with GLY 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ILE* 3.5 15.5 - - - +
89H ILE* 3.5 2.4 - - - -
90H SER* 2.9 32.1 + - - -
110H TYR* 4.3 13.6 - - - -
111H GLU* 1.3 76.4 - - - +
113H LYS* 1.3 60.5 + - - -
114H CYS* 3.1 6.6 + - - -
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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