Contacts of the strand formed by residues 104 - 109 (chain M) in PDB entry 2A3W
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 ILE 104 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L VAL* 3.8 30.1 - - + -
12L PRO* 3.9 17.0 - - + -
195L TYR* 4.6 1.3 - - - +
197L ILE* 4.1 17.3 - - + -
199L LYS* 4.2 13.9 - - + -
97M SER* 3.8 1.2 + - - +
98M TRP* 3.3 4.4 - - - -
99M GLU* 3.1 27.4 + - + +
102M SER* 3.1 26.4 + - - +
103M GLY* 1.3 75.8 - - - +
105M ALA* 1.3 64.4 + - - +
106M GLU* 4.2 7.6 + - + +
116M LYS* 3.9 27.6 - - + -
117M LYS 3.3 12.3 - - - +
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Residues in contact with ALA 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M LEU* 3.7 28.7 - - + -
80M VAL* 3.9 20.6 - - + -
96M VAL* 5.2 1.3 - - + -
97M SER 3.2 4.7 - - - -
98M TRP* 4.2 1.3 - - + -
103M GLY 3.4 0.8 + - - -
104M ILE* 1.3 73.2 - - - +
106M GLU* 1.3 61.2 + - - +
107M PHE* 4.1 5.7 + - + -
115M VAL 4.7 0.7 - - - +
116M LYS* 3.7 6.8 - - - +
117M LYS* 2.7 35.0 + - + +
119M LEU* 4.0 9.2 - - + -
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Residues in contact with GLU 106 (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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199L LYS* 4.9 6.1 - - - +
202L VAL* 5.6 2.0 - - + +
95M CYS 3.7 0.3 - - - +
96M VAL* 3.1 7.3 - - - -
97M SER* 2.8 49.9 + - - +
104M ILE* 4.2 8.9 - - + +
105M ALA* 1.3 71.0 - - - +
107M PHE* 1.3 62.7 + - - +
108M TRP* 2.9 37.9 + - + +
113M PRO* 6.5 0.4 - - + -
114M LEU 5.7 1.8 - - - +
116M LYS* 3.4 41.3 - - + +
163M VAL* 4.8 9.3 - - - +
164M LEU 4.6 9.4 - - - +
166M PRO* 5.8 1.6 - - - +
169M ILE* 5.8 0.2 - - - +
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Residues in contact with PHE 107 (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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63M VAL* 4.1 15.7 - - + -
71M TYR* 3.7 41.3 - - + -
72M SER 3.7 22.9 - - - -
73M LEU* 3.8 26.0 - - + -
80M VAL* 4.8 6.5 - - + -
82M SER* 4.5 12.8 - - - -
94M ILE* 4.3 11.4 - - + -
95M CYS 3.4 6.1 - - - -
96M VAL* 3.7 25.1 - - + -
105M ALA* 4.1 4.7 + - + -
106M GLU* 1.3 73.6 - - - +
108M TRP* 1.3 65.2 + - - +
109M ILE* 4.6 3.4 - - + -
113M PRO* 3.7 0.7 - - - +
114M LEU* 2.9 52.9 + - + +
115M VAL 5.5 1.8 + - - -
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Residues in contact with TRP 108 (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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202L VAL* 4.0 23.3 - - + -
93M HIS* 3.6 2.3 + - - +
94M ILE* 3.5 4.3 - - - -
95M CYS* 2.8 42.1 + - + +
96M VAL* 5.6 0.2 - - - -
97M SER* 5.5 1.1 - - - -
106M GLU* 2.9 43.3 + - + +
107M PHE* 1.3 78.8 + - - +
109M ILE* 1.3 63.1 + - - +
110M ASN 4.1 0.2 - - - -
111M GLY* 3.8 18.3 + - - -
112M THR 3.3 6.5 - - - +
113M PRO* 3.5 40.6 - - + -
165M PRO 5.6 0.2 - - - -
166M PRO* 3.7 43.1 - - + -
169M ILE* 3.7 45.3 - - + +
170M LEU* 5.9 3.6 - - + -
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Residues in contact with ILE 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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71M TYR* 3.6 33.0 - - + -
84M VAL* 4.2 19.9 - - + +
85M ILE 5.8 0.2 - - - +
86M GLU* 4.4 8.5 - - + +
92M VAL* 3.7 20.2 - - + -
93M HIS 3.5 1.3 - - - -
94M ILE* 3.8 23.3 - - + -
107M PHE* 4.6 5.8 - - + -
108M TRP* 1.3 79.0 - - - +
110M ASN* 1.3 79.4 + - - +
112M THR* 2.9 27.7 + - - -
114M LEU* 3.8 31.9 - - + -
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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