Contacts of the strand formed by residues 122 - 130 (chain C) in PDB entry 5DIR
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 VAL 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ALA 3.4 2.9 - - - +
53C TYR* 3.5 1.2 - - - -
54C ASN* 2.7 44.9 + - + +
112C ASN* 3.5 30.5 - - + +
115C ASP* 3.9 5.6 - - - +
116C ARG* 3.6 46.4 - - + +
121C HIS* 1.3 77.5 - - - +
123C VAL* 1.3 64.1 + - - +
124C ASP* 3.8 0.7 - - - +
140C ASN* 3.5 7.0 - - - +
203F SER* 3.4 30.7 - - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LYS* 3.6 37.5 - - + +
30C PHE* 5.7 0.2 - - + -
31C GLN* 3.2 33.0 - - + +
51C LEU* 3.8 16.4 - - + -
52C ALA 3.6 3.4 - - - +
53C TYR* 4.0 9.9 - - + -
115C ASP* 3.6 6.2 + - - +
119C LEU* 3.7 28.9 - - + -
121C HIS* 4.6 0.7 - - - +
122C VAL* 1.3 75.8 - - - +
124C ASP* 1.3 62.4 + - - +
125C PHE* 4.9 2.9 - - + -
140C ASN* 2.8 31.4 + - - +
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Residues in contact with ASP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 4.1 1.0 - - - +
51C LEU* 3.6 4.3 + - - +
52C ALA* 2.9 40.6 + - + +
54C ASN* 3.3 18.5 + - - +
122C VAL* 3.8 3.7 - - - +
123C VAL* 1.3 83.4 - - - +
125C PHE* 1.3 61.0 + - - +
138C ALA* 3.0 42.4 - - + +
139C PHE* 3.7 4.2 - - - -
140C ASN* 3.1 6.1 + - - -
203F SER* 2.5 36.4 + - - -
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 3.5 21.3 - - - -
27C LYS* 4.1 19.7 - - + -
30C PHE* 3.5 44.2 - + + -
49C TRP* 3.2 18.7 - + - -
50C THR* 2.7 46.2 + - - +
51C LEU* 5.1 1.1 - - + -
123C VAL* 4.6 2.0 - - + -
124C ASP* 1.3 77.1 - - - +
126C ILE* 1.3 84.8 + - + +
139C PHE 3.0 2.8 + - - -
140C ASN* 3.6 24.7 - - + -
141C LEU* 3.5 29.4 - - + -
204C OLC 6.5 0.7 - - + -
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.5 26.2 - - + -
48C SER 4.2 1.6 - - - -
49C TRP* 3.9 10.3 - - + -
125C PHE* 1.3 104.3 - - + +
127C LEU* 1.3 57.9 + - - +
128C VAL* 3.9 3.9 + - + -
138C ALA* 3.3 5.1 - - - -
139C PHE* 2.8 76.1 + - + +
140C ASN* 4.0 14.4 - - - +
141C LEU* 4.6 6.1 - - + +
144C SER* 4.5 3.8 - - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 4.2 26.7 - - - +
47C PHE* 3.6 1.5 - - - -
48C SER* 2.8 46.0 + - - +
50C THR* 3.8 24.0 - - + +
125C PHE 3.6 0.8 + - - -
126C ILE* 1.3 73.8 - - - +
128C VAL* 1.3 61.6 + - - +
129C HIS* 4.0 4.3 - - + -
135C TYR* 4.0 32.3 - - + -
136C PHE 3.3 24.7 - - - +
138C ALA* 4.3 14.6 - - + +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.3 11.0 - - + +
47C PHE* 3.8 24.0 - - + -
126C ILE* 3.9 10.8 + - + -
127C LEU* 1.3 73.2 - - - +
129C HIS* 1.3 63.2 + - - +
134C TRP* 4.8 3.8 - - + -
136C PHE* 3.0 58.4 + - + +
139C PHE* 3.9 13.7 - - + -
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Residues in contact with HIS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 4.1 8.4 + - - -
44C PRO 3.5 16.7 + - - -
45C ASP* 3.0 35.6 + - - +
46C LEU* 2.8 42.5 + - - +
47C PHE 4.2 0.2 - - - -
48C SER* 4.1 12.6 + - - -
127C LEU* 4.0 13.2 - - + -
128C VAL* 1.3 77.1 - - - +
130C TRP* 1.3 60.1 + - - +
131C GLN 2.7 27.3 + - - -
134C TRP* 3.3 26.5 - - - +
135C TYR* 3.4 34.1 - + + -
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Residues in contact with TRP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ASP* 4.5 11.0 - - + -
46C LEU* 3.8 27.6 - - + -
129C HIS* 1.3 77.0 - - - +
131C GLN* 1.3 95.8 + - + +
133C ARG* 3.0 39.1 + - + +
134C TRP* 3.0 42.0 + + + +
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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