Contacts of the strand formed by residues 104 - 109 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.8 17.7 - - + -
12G PRO* 3.8 27.4 - - + -
195G TYR* 4.5 1.8 - - - +
197G ILE* 4.2 17.5 - - + -
199G LYS* 4.4 9.9 - - + +
97H SER* 3.9 1.6 + - - +
98H TRP* 3.4 3.9 - - - -
99H GLU* 3.1 30.1 + - + +
102H SER* 3.1 24.7 + - - +
103H GLY* 1.3 75.8 - - - +
105H ALA* 1.3 62.4 + - - +
106H GLU* 4.2 6.7 + - + +
116H LYS* 3.8 33.9 - - + -
117H LYS 3.3 11.7 - - - +
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Residues in contact with ALA 105 (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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73H LEU* 3.7 30.1 - - + -
80H VAL* 3.9 21.1 - - + -
82H SER* 5.6 0.7 + - - -
96H VAL* 5.2 1.6 - - + -
97H SER 3.3 4.5 - - - -
98H TRP* 4.2 1.8 - - + -
103H GLY 3.4 1.0 + - - -
104H ILE* 1.3 74.4 - - - +
106H GLU* 1.3 59.9 + - - +
107H PHE* 4.2 4.7 + - + -
115H VAL 4.6 0.9 - - - +
116H LYS* 3.6 6.2 - - - +
117H LYS* 2.7 33.5 + - + +
119H LEU* 4.0 8.1 - - + -
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Residues in contact with GLU 106 (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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199G LYS* 5.1 4.0 + - - +
202G VAL* 5.5 2.4 - - - +
95H CYS 3.5 0.5 - - - +
96H VAL* 3.2 6.7 - - - +
97H SER* 2.9 48.6 + - - +
104H ILE* 4.2 6.5 - - + +
105H ALA* 1.3 71.4 - - - +
107H PHE* 1.3 62.2 + - - +
108H TRP* 2.9 35.4 + - + +
113H PRO* 6.4 0.7 - - + -
114H LEU 5.6 3.1 - - - +
116H LYS* 3.3 46.2 + - + +
163H VAL* 4.9 7.3 - - - +
164H LEU 4.7 9.4 - - - +
166H PRO* 5.8 1.4 - - - +
169H ILE* 5.4 0.3 - - - +
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Residues in contact with PHE 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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63H VAL* 4.2 16.4 - - + -
71H TYR* 3.6 41.3 - - + -
72H SER 3.7 22.2 - - - -
73H LEU* 3.7 24.9 - - + -
80H VAL* 4.9 6.5 - - + -
82H SER* 4.2 15.2 + - - -
94H ILE* 4.3 14.1 - - + -
95H CYS 3.4 5.2 - - - -
96H VAL* 3.7 25.6 - - + -
105H ALA* 4.2 3.0 + - + -
106H GLU* 1.3 74.0 - - - +
108H TRP* 1.3 58.7 + - - +
109H ILE* 4.4 4.5 - - + -
113H PRO* 3.6 2.9 - - - +
114H LEU* 2.8 57.5 + - + +
115H VAL 5.4 2.2 + - - -
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Residues in contact with TRP 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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202G VAL* 4.0 20.0 - - + -
93H HIS* 3.5 2.3 + - - +
94H ILE* 3.5 4.7 - - - -
95H CYS* 2.6 42.8 + - + +
96H VAL* 5.6 0.2 - - - -
97H SER* 5.4 0.7 - - - -
106H GLU* 2.9 42.3 + - + +
107H PHE* 1.3 77.3 - - - +
109H ILE* 1.3 62.7 + - - +
110H ASN 4.1 0.4 + - - -
111H GLY* 3.7 19.2 + - - -
112H THR 3.3 5.2 - - - +
113H PRO* 3.6 44.4 - - + -
166H PRO* 3.6 42.0 - - + -
169H ILE* 3.6 45.1 - - + +
170H LEU* 4.9 8.1 - - + -
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Residues in contact with ILE 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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71H TYR* 3.6 33.0 - - + -
84H VAL* 4.1 25.4 - - + +
85H ILE 5.9 0.2 - - - +
86H GLU* 4.2 7.6 - - + +
92H VAL* 3.6 22.0 - - + -
93H HIS 3.4 1.3 - - - -
94H ILE* 3.9 20.0 - - + -
107H PHE* 4.4 7.6 - - + -
108H TRP* 1.3 78.8 - - - +
110H ASN* 1.3 80.4 + - - +
112H THR* 2.8 27.4 + - - -
114H LEU* 3.7 27.6 - - + -
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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