Contacts of the strand formed by residues 118 - 121 (chain O) in PDB entry 2D2I
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 LYS 118 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93O ASP 2.9 7.2 + - - +
94O LEU* 3.3 23.4 - - + -
95O VAL* 3.0 27.0 + - - +
112O ILE* 4.8 0.2 - - - -
116O ALA 3.5 0.6 - - - -
117O LYS* 1.3 80.7 - - + +
119O VAL* 1.3 71.1 + - - +
142O TYR* 2.9 29.3 + - - +
143O ARG 4.3 1.6 + - - -
144O HIS* 2.5 49.3 + - + +
147O PHE 2.7 24.5 + - - +
148O ALA* 3.3 11.9 - - - +
150O ILE* 3.9 18.4 - - + +
333O ALA* 5.1 3.6 - - + -
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Residues in contact with VAL 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O LEU* 4.3 0.9 - - - -
95O VAL* 3.4 15.9 - - + +
97O GLU* 4.0 19.3 - - + -
108O ALA* 3.4 45.8 - - + +
111O HIS* 4.0 9.2 - - + -
112O ILE* 3.6 22.0 - - + -
118O LYS* 1.3 78.1 - - - +
120O LEU* 1.3 60.6 + - - +
121O ILE* 4.3 4.9 - - + -
148O ALA 2.9 11.2 + - - +
149O VAL* 3.4 5.1 - - + -
150O ILE* 2.9 30.5 + - - +
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Residues in contact with LEU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O LEU* 4.0 9.3 - - + +
95O VAL 2.9 11.3 + - - +
96O ILE* 3.6 10.4 - - + -
97O GLU* 2.8 28.3 + - - -
119O VAL* 1.3 72.0 - - - +
121O ILE* 1.3 72.9 + - - +
122O THR* 3.6 2.6 + - + +
150O ILE* 3.4 22.9 - - + +
152O ASN* 4.1 6.5 - - + +
326O VAL* 3.8 35.0 - - + +
329O LEU* 3.6 31.0 - - + -
330O ALA* 3.9 22.9 - - + +
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Residues in contact with ILE 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O GLU* 3.5 13.2 - - + +
102O PHE 3.7 20.6 - - - +
103O VAL* 3.7 44.9 - - + +
104O THR 4.4 0.2 - - - +
108O ALA* 4.0 8.3 - - + -
119O VAL* 4.3 3.4 - - + -
120O LEU* 1.3 74.7 - - - +
122O THR* 1.3 61.4 + - - +
123O ALA* 3.1 24.8 + - + +
124O PRO 4.5 0.2 - - - +
125O GLY* 4.6 8.3 - - - -
130O VAL* 4.6 3.6 - - + -
149O VAL* 3.6 28.0 - - + -
150O ILE 2.7 16.1 + - - +
151O SER* 3.5 2.3 - - - -
152O ASN 3.3 21.8 + - - -
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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