Contacts of the strand formed by residues 120 - 124 (chain C) in PDB entry 4LDD
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 TYR 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASN 3.6 1.9 - - - +
50C PRO* 3.2 5.4 - - - +
51C LEU 3.1 30.0 + - - +
53C PRO* 3.8 9.6 - - + -
75C LEU* 5.0 4.7 - - + -
114C ALA 3.8 0.5 + - - -
115C ILE* 2.5 50.3 + - + +
118C ALA* 3.3 19.9 - - + +
119C SER* 1.3 79.1 - - - +
121C THR* 1.3 65.2 + - - +
122C ILE* 6.2 0.2 - - + -
135C VAL* 4.3 11.7 - - + -
136C ASN 3.3 6.7 - - - +
137C ARG* 3.5 43.9 + - + -
138C LEU 4.8 0.2 - - - +
149C LEU* 3.9 22.4 - - + +
150C LEU* 4.2 1.9 - - - +
176C LEU* 3.9 7.5 - - + +
179C LEU* 3.7 27.1 - - + -
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Residues in contact with THR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 4.2 13.9 - - + +
48C SER* 3.3 27.4 - - - +
49C ASN 4.2 0.2 - - - -
50C PRO* 3.8 18.6 - - + -
120C TYR* 1.3 78.9 - - - +
122C ILE* 1.3 66.3 + - - +
134C ARG 4.6 0.2 - - - -
135C VAL* 3.3 7.6 - - - +
136C ASN* 2.9 54.8 + - - +
138C LEU* 4.4 17.6 - - + +
176C LEU* 5.1 0.4 - - - -
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Residues in contact with ILE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR 4.6 0.9 - - - +
47C PRO* 3.6 0.3 - - - +
48C SER* 2.6 48.4 + - - +
77C ALA* 5.0 5.2 - - + -
79C VAL* 4.9 6.3 - - + -
94C ILE* 4.6 3.4 - - + -
96C LEU* 3.8 19.5 - - + -
120C TYR* 6.2 0.4 - - + -
121C THR* 1.3 83.5 - - - +
123C THR* 1.3 62.1 + - - +
133C VAL* 3.7 19.7 - - + -
134C ARG 3.7 0.7 - - - +
135C VAL* 3.7 24.7 - - + +
174C PHE* 3.5 36.6 + - + -
176C LEU* 4.7 21.8 - - + -
179C LEU* 6.5 0.4 - - + -
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP 6.4 0.9 - - - -
46C THR 4.8 1.3 - - - -
47C PRO* 3.6 28.0 - - + -
121C THR* 4.8 0.4 - - - +
122C ILE* 1.3 78.5 - - - +
124C HIS* 1.3 60.0 + - - +
125C PHE* 4.3 13.7 - - - -
133C VAL* 3.3 9.7 - - - +
134C ARG* 2.7 67.0 + - - +
136C ASN* 3.5 30.7 - - - +
174C PHE* 4.3 2.9 - - - -
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Residues in contact with HIS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 3.7 23.7 + - - +
46C THR 4.9 7.2 + - - +
122C ILE 4.4 0.2 + - - -
123C THR* 1.3 71.4 - - - +
125C PHE* 1.3 94.9 + - - +
131C PRO* 4.6 1.0 - - - +
132C LEU 3.7 6.5 - - - -
133C VAL* 4.6 3.8 - - + -
159C GLN* 3.1 24.7 + - - -
169C PRO 5.1 0.4 + - - -
170C GLN* 3.2 25.8 - - - -
171C TYR* 4.7 1.7 - + - -
172C PHE* 3.3 57.6 + + - +
173C THR* 5.2 0.9 - - - -
174C PHE* 3.5 22.3 - + + -
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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
------------------------------------------------------------
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