Contacts of the strand formed by residues 117 - 122 (chain D) in PDB entry 2W3S
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 ARG 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D GLY 4.0 0.9 - - - +
50D LEU* 3.8 1.2 + - - -
51D ASP* 2.9 64.7 + - + +
53D GLU* 5.7 0.4 - - - +
54D PRO* 3.4 25.3 - - + +
115D LYS 3.6 0.9 + - - +
116D ALA* 1.3 70.8 - - - +
118D ILE* 1.3 61.9 + - - +
119D THR* 4.3 2.2 + - + -
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Residues in contact with ILE 118 (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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39D LEU 4.9 4.5 - - - +
47D ILE* 4.3 9.9 - - + -
49D GLY 3.6 10.3 - - - +
50D LEU* 3.8 23.3 - - + -
98D ILE* 3.9 16.6 - - + -
99D PHE* 4.2 16.4 - - + -
116D ALA* 3.7 15.0 + - + +
117D ARG* 1.3 78.4 - - - +
119D THR* 1.3 72.9 + - - +
120D TYR* 3.5 51.6 - - + +
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Residues in contact with THR 119 (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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47D ILE* 3.6 4.2 - - - +
48D THR* 2.7 43.1 + - - +
49D GLY* 2.8 41.0 + - - +
117D ARG* 5.7 2.2 - - + -
118D ILE* 1.3 78.2 - - - +
120D TYR* 1.3 59.1 + - - +
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Residues in contact with TYR 120 (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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39D LEU 4.1 1.6 + - - -
40D SER* 3.7 7.3 - - - -
41D THR* 3.0 39.5 + - - +
42D GLU* 3.4 26.7 - - + -
45D ALA* 3.7 11.9 - - + -
46D ALA 3.1 7.4 - - - +
47D ILE* 4.3 9.2 - - + -
48D THR* 3.7 5.8 + - - -
91D VAL* 4.0 24.5 - - + -
98D ILE* 3.8 13.6 - - + +
118D ILE* 3.5 42.7 - - + +
119D THR* 1.3 77.5 - - - +
121D ALA* 1.3 61.9 + - - +
122D PRO* 3.3 14.0 - - + +
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Residues in contact with ALA 121 (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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45D ALA* 3.4 0.7 - - - -
46D ALA* 2.6 41.4 + - + +
48D THR* 3.7 13.7 + - - +
120D TYR* 1.3 73.4 - - - +
122D PRO* 1.3 70.0 - - - +
123D ARG* 3.7 4.5 - - - +
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Residues in contact with PRO 122 (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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42D GLU* 3.9 24.5 - - - +
44D SER 3.8 0.9 - - - +
45D ALA* 3.6 10.3 - - + -
120D TYR* 3.3 14.1 - - + +
121D ALA* 1.3 88.4 - - - +
123D ARG* 1.3 62.8 + - - +
124D PRO* 5.0 0.3 - - - +
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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