Contacts of the strand formed by residues 258 - 266 (chain I) in PDB entry 5TJ4
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 PHE 258 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112I ALA* 4.7 2.3 - - - -
113I LEU 4.9 0.2 + - - -
155I TYR* 3.5 33.6 + - + +
158I TRP* 3.1 45.0 - + + -
159I PRO* 5.1 0.8 - - - +
168I ALA* 3.8 23.6 - - + -
256I LYS 3.6 1.4 + - - -
257I PRO* 1.3 78.9 - - - +
259I VAL* 1.3 59.2 + - - +
328I GLU* 3.5 23.8 - - + -
329I ILE 4.3 2.5 - - - -
330I MET* 3.3 28.5 - - + -
331I PRO* 3.9 24.0 - - + -
336I MET* 4.7 2.0 - - + -
339I PHE* 3.8 18.2 - + - -
340I TRP* 3.6 21.1 - + + -
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Residues in contact with VAL 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I HIS* 3.5 6.6 - - - -
110I VAL* 5.1 6.7 - - + -
111I GLU 3.8 7.4 - - - +
112I ALA* 3.8 11.0 - - + -
257I PRO* 3.9 7.6 - - + +
258I PHE* 1.3 76.6 - - - +
260I GLY* 1.3 59.5 + - - +
324I ALA* 3.6 42.4 - - + +
328I GLU 3.0 7.4 + - - +
329I ILE* 2.6 53.9 - - + +
330I MET* 3.1 20.2 + - - +
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Residues in contact with GLY 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I ALA* 4.5 6.1 - - - -
64I HIS* 4.0 2.0 - - - -
110I VAL* 3.5 4.2 - - - +
111I GLU* 2.9 45.0 + - - +
155I TYR* 4.2 2.7 + - - -
258I PHE 4.1 1.4 + - - -
259I VAL* 1.3 74.2 - - - +
261I VAL* 1.3 63.4 + - - +
262I LEU 3.8 1.1 - - - -
330I MET* 3.3 21.9 - - - +
1S GLC 5.2 0.2 - - - -
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Residues in contact with VAL 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I ALA* 4.1 0.7 - - - -
64I HIS* 2.9 32.1 + - + +
92I PHE* 5.2 0.4 - - + -
93I THR* 4.5 11.7 - - + +
96I ALA* 3.7 27.6 - - + -
107I PRO* 3.9 21.3 - - + -
109I ALA 3.2 15.0 - - - +
110I VAL* 4.4 14.6 - - + -
260I GLY* 1.3 74.8 - - - +
262I LEU* 1.3 65.7 + - - +
263I SER* 2.8 25.4 + - - +
329I ILE* 4.0 18.6 - - + -
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Residues in contact with LEU 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 5.0 10.3 - - + -
12I ASN* 6.3 2.7 - - + -
15I LYS* 5.4 8.7 - - + -
61I PHE* 4.0 25.1 - - + +
62I TRP* 3.7 19.7 - - - +
63I ALA* 4.1 5.1 - - - +
108I ILE* 2.8 58.8 + - + +
109I ALA* 2.7 20.7 + - + +
111I GLU* 3.8 26.2 - - - +
260I GLY 3.8 2.8 + - - -
261I VAL* 1.3 71.7 - - - +
263I SER* 1.3 55.9 + - - +
299I LEU* 4.3 17.0 - - + -
1S GLC 5.1 4.3 - - - +
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Residues in contact with SER 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I ILE 3.4 1.7 - - - +
61I PHE* 3.3 5.7 - - - -
62I TRP 2.8 34.9 + - - +
64I HIS* 3.8 4.6 - - - +
67I PHE* 3.4 9.4 - - - -
97I VAL* 3.2 30.1 - - - +
105I ALA* 4.0 8.3 - - - -
106I TYR 3.2 10.3 - - - -
107I PRO* 3.9 0.7 - - - +
108I ILE* 4.2 3.1 - - - -
261I VAL* 2.8 20.9 + - - +
262I LEU* 1.3 74.1 + - - +
264I ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ILE* 4.0 3.1 - - + -
60I ILE 3.2 6.1 - - - -
61I PHE* 3.6 36.3 - - + -
105I ALA* 3.3 2.4 - - - -
106I TYR* 2.7 47.5 + - + +
108I ILE* 4.1 4.9 - - + +
263I SER* 1.3 73.0 - - - +
265I GLY* 1.3 58.5 + - - +
280I LEU* 3.8 20.0 - - + -
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Residues in contact with GLY 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ASP 3.8 0.2 - - - +
59I ILE* 3.3 5.1 - - - -
60I ILE* 2.8 40.8 + - - +
67I PHE* 3.6 19.9 - - - -
76I LEU* 4.2 4.0 - - - -
104I ILE 4.1 6.1 - - - -
105I ALA* 4.1 6.1 - - - -
264I ALA* 1.3 74.6 - - - +
266I ILE* 1.3 63.9 + - - -
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Residues in contact with ILE 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ASP 3.4 9.2 - - - +
59I ILE* 4.6 2.0 - - + -
76I LEU* 3.5 6.5 - - - +
77I ALA* 2.8 40.6 + - + -
79I ILE* 3.7 27.8 - - + +
104I ILE 4.7 1.2 + - - -
106I TYR* 4.2 11.0 - - + -
265I GLY* 1.3 73.7 - - - +
267I ASN* 1.3 66.1 + - - +
270I SER* 4.8 3.1 - - - +
273I LYS* 3.9 27.1 - - + +
276I ALA* 3.8 31.2 - - + -
277I LYS* 4.1 13.5 - - + +
280I LEU* 4.2 12.1 - - + -
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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