Contacts of the strand formed by residues 108 - 115 (chain M) in PDB entry 6NMY
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 GLU 108 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104M TRP* 4.5 17.5 - - - -
106M GLY 4.1 10.2 + - - +
107M ALA* 1.3 79.4 - - - +
109M ASN* 1.3 74.2 + - - +
110M LEU 3.1 4.1 + - - +
124M TRP* 3.4 1.6 - - - +
125M ALA* 2.8 39.8 + - + +
127M GLY* 5.5 1.8 - - - -
128M PRO* 4.2 21.0 - - + +
196M THR* 4.8 4.7 - - + -
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Residues in contact with ASN 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M GLU* 1.3 83.8 - - - +
110M LEU* 1.3 63.2 + - - +
111M THR* 3.3 10.3 + - - +
123M SER 3.2 11.3 - - - +
124M TRP* 3.6 2.9 - - - -
125M ALA* 4.6 12.1 - - + +
196M THR* 5.8 0.2 - - - +
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M ALA* 5.6 0.7 - - + -
108M GLU 3.1 2.1 - - - +
109M ASN* 1.3 75.7 - - - +
111M THR* 1.3 56.0 + - - +
112M CYS* 4.0 19.1 - - - -
123M SER 3.4 6.5 - - - +
124M TRP* 3.8 22.7 - - + -
138M LEU* 5.1 0.2 - - + -
182M ILE* 4.6 11.9 - - + -
184M VAL* 3.6 34.8 - - + -
196M THR* 4.3 25.7 - - + +
197M ASP 4.9 2.0 - - - +
198M LYS* 2.6 68.3 + - + +
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Residues in contact with THR 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M ASN 3.7 8.2 + - - +
110M LEU* 1.3 78.5 - - - +
112M CYS* 1.3 63.0 + - - +
113M TRP* 3.5 10.6 - - - -
122M CYS* 3.4 0.7 - - - -
123M SER* 2.9 43.4 + - - -
198M LYS* 3.8 12.8 - - - +
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Residues in contact with CYS 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 4.0 19.7 - - + -
111M THR* 1.3 76.1 - - - +
113M TRP* 1.3 64.0 + - - +
120M LEU* 4.3 5.2 - - + -
121M SER 3.3 3.6 - - - +
122M CYS* 2.0 47.6 - - - -
182M ILE* 3.5 25.1 - - + -
198M LYS* 4.9 4.9 - - - +
200M VAL* 4.5 12.2 - - + +
205M ILE* 3.7 19.9 - - + +
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Residues in contact with TRP 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M THR* 3.5 26.0 - - - -
112M CYS* 1.3 76.5 - - - +
114M ILE* 1.3 63.0 + - - +
115M HIS* 4.0 23.8 + + + +
119M PHE 3.9 0.3 - - - +
120M LEU* 3.7 5.7 - - - +
121M SER* 2.9 68.2 + - - -
122M CYS 4.5 0.7 - - - -
123M SER* 3.8 27.6 - - - -
155M LYS* 6.3 0.4 - - - -
205M ILE* 3.4 17.0 - - + +
207M ILE* 3.4 28.7 - - + -
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Residues in contact with ILE 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M TRP* 1.3 72.9 - - - +
115M HIS* 1.3 63.6 + - - +
117M VAL 4.3 8.5 - - - +
119M PHE 3.3 20.4 - - - +
120M LEU* 3.7 14.8 - - + -
170M ILE* 4.4 8.5 - - + -
202M PHE* 3.5 32.8 - - + +
205M ILE* 2.9 19.6 + - + +
206M GLU* 4.0 17.7 - - + -
207M ILE* 2.7 34.8 + - - +
232M PHE* 3.4 37.2 - - + -
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Residues in contact with HIS 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M TRP* 4.0 22.2 + + + -
114M ILE* 1.3 79.0 - - - +
116M ASP* 1.3 80.1 + - - +
117M VAL* 3.1 1.3 + - - -
118M ASP 3.8 0.3 + - - -
119M PHE* 2.8 75.2 + + + +
121M SER* 2.5 30.4 + - - -
155M LYS* 5.9 1.8 - - - -
166M ARG* 4.3 9.1 - - - +
206M GLU* 6.1 0.2 - - - -
207M ILE* 4.2 17.5 - - + -
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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