Contacts of the helix formed by residues 2419 - 2428 (chain B) in PDB entry 1I4E
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 THR2419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A TRP* 5.2 0.2 - - - -
2260B ARG* 4.5 4.0 - - - +
2262B GLY 6.1 0.2 - - - -
2263B THR* 5.6 1.6 - - - -
2266B ASP* 2.7 33.2 + - + +
2315B LEU* 6.3 0.2 - - + -
2358B GLN* 2.7 40.7 + - + +
2412B TYR 3.5 9.4 - - - -
2413B ARG* 3.1 35.2 - - + +
2418B GLY* 1.3 73.7 - - - -
2420B TRP* 1.3 63.2 + - - +
2422B ILE* 3.2 13.9 + - - +
2423B GLN* 2.9 24.5 + - - +
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Residues in contact with TRP2420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 3.5 36.5 + - - -
254A TRP* 4.1 12.5 - + + -
2412B TYR* 3.3 55.6 + + + +
2413B ARG 5.0 0.2 - - - -
2414B ASN* 4.8 2.1 - - + +
2418B GLY 4.4 7.4 - - - -
2419B THR* 1.3 74.4 - - - +
2421B TYR* 1.3 59.3 + - - +
2423B GLN* 3.8 0.7 - - - +
2424B SER* 2.9 35.6 + - - -
2450B VAL* 4.1 11.7 - - + -
2453B LYS* 3.6 49.0 - - + +
2454B ASP* 4.0 6.1 - - - -
2455B ASP* 3.8 22.9 - - - -
2460B GLY 4.9 0.2 - - - -
2461B LYS 4.8 0.4 - - - -
2462B GLN* 3.6 36.1 - - + +
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Residues in contact with TYR2421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2356B PHE* 3.4 27.2 - + + -
2357B ILE 4.8 2.7 - - - -
2358B GLN* 4.0 5.1 - - + +
2402B GLY* 3.0 38.0 - - - -
2403B MET 4.2 1.1 - - - -
2404B ALA* 3.3 42.0 - - + +
2419B THR* 3.5 0.8 + - - -
2420B TRP* 1.3 79.3 - - - +
2422B ILE* 1.3 63.5 + - + +
2424B SER* 3.1 2.1 + - - -
2425B LEU* 2.7 47.7 + - + +
2443B LEU* 4.3 10.6 - - + +
2446B VAL* 3.8 24.2 - - + -
2447B ASN* 5.3 0.9 - - - -
2450B VAL* 4.1 6.7 - - - -
2462B GLN* 3.9 11.1 - - - +
2464B PRO* 3.9 22.2 - - + -
2466B PRO* 5.7 0.2 - - - +
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Residues in contact with ILE2422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2266B ASP* 3.3 30.1 - - + +
2269B ALA* 4.8 1.1 - - + -
2270B LEU* 3.6 41.7 - - + -
2313B CYS* 5.3 0.2 - - - -
2315B LEU* 3.7 25.1 - - + -
2356B PHE* 4.9 7.2 - - + -
2358B GLN* 3.9 13.7 - - + +
2419B THR* 3.2 19.1 + - - +
2421B TYR* 1.3 89.0 - - + +
2423B GLN* 1.3 60.5 + - - +
2425B LEU* 3.5 11.5 + - + +
2426B CYS* 3.0 33.7 + - - -
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Residues in contact with GLN2423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TRP* 3.6 42.5 - - + +
2265B LEU* 4.6 1.6 + - - +
2266B ASP* 3.5 18.6 + - - +
2269B ALA* 4.0 16.6 - - - +
2417B GLU* 2.6 32.9 + - - +
2418B GLY 4.0 0.7 - - - -
2419B THR 2.9 30.6 + - - +
2420B TRP 3.8 0.2 - - - +
2422B ILE* 1.3 75.6 - - - +
2424B SER* 1.3 59.8 + - - +
2426B CYS* 3.2 4.9 + - - +
2427B GLN* 2.8 31.5 + - - +
2430B ARG* 5.7 2.8 + - - -
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Residues in contact with SER2424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TRP* 3.2 26.4 - - - -
2420B TRP 2.9 19.8 + - - -
2421B TYR 3.7 2.2 - - - -
2423B GLN* 1.3 71.0 - - - +
2425B LEU* 1.3 60.5 + - - +
2426B CYS 2.9 4.7 - - - -
2427B GLN* 4.4 3.8 - - - +
2428B SER* 2.6 39.1 + - - -
2446B VAL* 3.9 18.8 - - - -
2449B GLU* 3.8 19.2 - - - +
2450B VAL* 3.9 6.6 - - - +
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Residues in contact with LEU2425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2270B LEU* 4.3 17.0 - - + -
2274B PHE* 5.3 0.2 - - + -
2356B PHE* 3.5 56.1 - - + -
2421B TYR* 2.7 31.6 + - + +
2422B ILE* 3.6 13.7 - - + +
2423B GLN 3.3 0.2 - - - -
2424B SER* 1.3 72.4 - - - +
2426B CYS* 1.3 52.7 + - - +
2429B LEU* 2.7 51.0 - - + +
2439B ILE* 5.9 1.1 - - + -
2442B ILE* 5.0 1.7 - - + +
2443B LEU* 3.9 21.1 - - + -
2446B VAL* 4.1 10.5 - - + +
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Residues in contact with CYS2426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2269B ALA* 4.2 13.0 - - + +
2270B LEU* 3.1 32.1 - - - -
2273B THR* 3.3 27.1 - - - +
2274B PHE* 5.7 0.2 - - - -
2422B ILE* 3.0 23.6 - - - +
2423B GLN* 3.2 6.6 + - - +
2424B SER 2.9 0.4 - - - -
2425B LEU* 1.3 80.2 - - - +
2427B GLN* 1.3 59.4 + - - +
2428B SER 2.8 6.2 + - - -
2429B LEU* 4.0 3.4 - - - -
2430B ARG* 2.6 43.6 + - - +
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Residues in contact with GLN2427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A SER 5.1 0.3 - - - +
254A TRP* 3.6 52.7 - - + +
255A GLY 4.8 0.7 - - - +
2423B GLN 2.8 19.7 + - - +
2424B SER* 4.4 1.6 - - - +
2426B CYS* 1.3 71.8 - - - +
2428B SER* 1.3 66.3 + - - +
2430B ARG* 4.1 32.7 + - - +
2431B GLU* 3.5 18.2 - - - +
2445B GLU* 5.4 1.0 + - - -
2449B GLU* 5.2 7.1 - - - +
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Residues in contact with SER2428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2424B SER* 2.6 28.9 + - - -
2426B CYS 2.8 0.8 - - - -
2427B GLN* 1.3 86.9 + - - +
2429B LEU* 1.3 57.3 + - - +
2431B GLU* 3.9 4.5 - - - +
2432B ARG* 3.1 31.7 + - - +
2442B ILE* 3.8 8.4 - - - +
2445B GLU* 2.9 32.6 + - - +
2446B VAL* 4.0 16.5 - - - +
2449B GLU* 4.6 4.3 - - - +
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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