Contacts of the helix formed by residues 2409 - 2426 (chain B) in PDB entry 2H7C
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 ASP2409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2407B THR* 3.1 16.0 + - - +
2408B ASP* 1.3 76.5 - - - +
2410B THR* 1.3 54.7 + - - +
2411B VAL* 2.9 29.4 + - - +
2412B LYS* 2.7 60.5 + - + +
2413B LYS* 2.8 12.5 + - - +
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Residues in contact with THR2410 (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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2372B GLN* 3.2 27.2 - - + +
2373B LEU 2.7 44.7 + - - +
2374B ASP* 4.5 9.2 - - + +
2408B ASP* 2.9 19.6 + - - +
2409B ASP* 1.3 70.7 + - - +
2411B VAL* 1.3 62.8 + - - +
2413B LYS* 3.8 5.4 - - + -
2414B LYS 3.2 10.4 + - - -
4463D THR* 6.0 3.6 - - + -
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Residues in contact with VAL2411 (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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2371B GLY 3.2 18.6 - - - +
2372B GLN* 4.4 9.4 - - + +
2409B ASP* 2.9 15.0 + - - +
2410B THR* 1.3 83.2 - - - +
2412B LYS* 1.3 64.7 + - + +
2414B LYS* 3.3 17.5 + - - +
2415B ASP* 3.4 21.8 + - - +
4372D GLN* 5.2 2.9 - - - +
4411D VAL* 4.3 25.4 - - + -
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Residues in contact with LYS2412 (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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2407B THR* 4.1 19.4 + - + +
2409B ASP* 2.7 45.9 + - + +
2411B VAL* 1.3 72.6 - - + +
2413B LYS* 1.3 63.7 + - - +
2415B ASP* 3.3 7.9 + - - +
2416B LEU* 3.0 33.6 + - + +
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Residues in contact with LYS2413 (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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2373B LEU* 3.3 25.8 - - - +
2374B ASP* 4.6 2.2 - - - +
2375B GLN* 3.1 36.9 + - + +
2404B LEU* 2.7 50.0 + - + +
2405B GLY* 4.3 1.6 - - - -
2407B THR* 2.6 32.2 + - + +
2408B ASP* 3.8 20.8 - - - +
2409B ASP 2.8 13.0 + - - +
2410B THR* 3.7 8.3 - - + +
2412B LYS* 1.3 77.1 - - - +
2414B LYS* 1.3 56.5 + - - +
2416B LEU* 4.4 2.7 - - - -
2417B PHE* 2.9 27.1 + - - +
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Residues in contact with LYS2414 (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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2368B LEU* 4.8 16.3 - - + +
2371B GLY* 3.3 37.4 + - - +
2373B LEU* 3.9 23.1 - - + +
2410B THR 3.2 6.2 + - - +
2411B VAL* 3.4 9.5 - - - +
2413B LYS* 1.3 80.3 - - - +
2415B ASP* 1.3 94.8 + - - +
2417B PHE* 3.2 12.3 + - - +
2418B LEU* 3.2 18.7 + - + +
4369D SER 4.8 0.4 - - - +
4370D GLU* 2.9 50.7 + - - +
4372D GLN* 3.7 20.2 + - - +
4411D VAL* 5.9 0.2 - - - +
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Residues in contact with ASP2415 (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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2353B GLN* 5.6 2.8 + - - -
2411B VAL* 3.4 18.6 + - - +
2412B LYS* 3.3 10.5 + - - +
2414B LYS* 1.3 103.5 + - - +
2416B LEU* 1.3 63.2 + - + +
2418B LEU* 3.3 10.8 + - - +
2419B ASP* 3.1 27.8 + - - +
4370D GLU* 3.5 11.3 - - - +
4372D GLN* 5.2 1.2 + - - +
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Residues in contact with LEU2416 (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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2403B TYR* 3.1 31.6 - - + +
2404B LEU* 3.4 19.5 - - + +
2406B GLY* 5.9 0.9 - - - +
2407B THR* 4.0 24.5 - - + -
2412B LYS* 3.0 25.6 + - + +
2415B ASP* 1.3 75.2 - - + +
2417B PHE* 1.3 59.9 + - - +
2419B ASP* 3.3 20.8 + - + +
2420B LEU* 3.0 26.7 + - - +
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Residues in contact with PHE2417 (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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2366B TYR* 3.4 35.9 - + - -
2368B LEU* 4.6 5.2 - - + -
2373B LEU* 3.7 17.3 - - + -
2378B ALA* 3.5 34.3 - - + -
2381B LEU* 3.8 23.6 - - + -
2382B LEU* 4.0 26.7 - - + -
2400B THR* 5.6 1.3 - - + -
2404B LEU* 3.9 9.4 - - + -
2413B LYS 2.9 13.7 + - - +
2414B LYS 3.3 9.6 - - - +
2415B ASP 3.1 0.2 - - - -
2416B LEU* 1.3 76.1 - - - +
2418B LEU* 1.3 74.8 + - + +
2420B LEU* 3.2 16.3 + - + +
2421B ILE* 3.2 26.9 + - + +
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Residues in contact with LEU2418 (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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2353B GLN* 5.6 1.6 - - - +
2355B PHE* 3.7 42.9 - - + +
2356B GLY* 4.3 2.9 - - - +
2366B TYR* 5.5 0.4 - - + -
2368B LEU* 3.6 27.4 - - + -
2414B LYS* 3.2 17.6 + - - +
2415B ASP* 3.3 14.1 + - - +
2417B PHE* 1.3 82.3 - - + +
2419B ASP* 1.3 65.9 + - - +
2421B ILE* 3.5 3.4 + - - +
2422B ALA* 3.1 23.2 + - - +
4369D SER* 4.7 9.9 - - - +
4370D GLU* 3.4 37.7 - - - +
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Residues in contact with ASP2419 (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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2352B LYS 4.8 8.8 - - - +
2353B GLN* 5.3 8.1 - - - +
2403B TYR* 4.5 9.4 - - + -
2415B ASP* 3.1 19.4 + - - +
2416B LEU* 3.4 26.2 - - + +
2417B PHE 3.2 0.4 - - - -
2418B LEU* 1.3 76.9 - - - +
2420B LEU* 1.3 54.5 + - - +
2422B ALA* 3.2 6.9 + - - +
2423B ASP* 2.8 44.9 + - - +
2540B LYS* 6.1 1.8 - - - +
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Residues in contact with LEU2420 (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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2382B LEU* 4.2 35.7 - - + -
2391B ILE* 4.4 1.1 - - + -
2399B ALA 3.9 23.6 - - - +
2400B THR* 4.6 4.5 - - - -
2403B TYR* 3.6 28.2 - - + -
2404B LEU* 5.9 0.7 - - + -
2416B LEU 3.0 13.2 + - - +
2417B PHE* 3.4 22.0 - - + +
2419B ASP* 1.3 76.1 - - - +
2421B ILE* 1.3 65.5 + - + +
2423B ASP* 3.3 2.4 + - - +
2424B VAL* 3.2 24.6 + - + +
2547B TRP* 3.3 30.0 - - + -
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Residues in contact with ILE2421 (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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2355B PHE* 3.5 46.9 - - + -
2366B TYR* 4.4 10.8 - - - +
2382B LEU* 3.6 31.4 - - + -
2385B SER* 4.4 7.0 - - - -
2388B LEU* 4.9 2.5 - - + -
2389B VAL* 3.7 17.7 - - + -
2417B PHE* 3.2 25.4 + - + +
2418B LEU* 3.9 5.8 - - - +
2419B ASP 3.3 0.2 - - - -
2420B LEU* 1.3 77.8 - - + +
2422B ALA* 1.3 56.9 + - - +
2424B VAL* 3.3 1.9 + - - +
2425B MET* 3.0 43.1 + - + +
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Residues in contact with ALA2422 (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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2352B LYS 5.6 2.2 - - - +
2353B GLN* 5.0 2.5 - - - -
2354B GLU* 3.9 19.0 - - + +
2355B PHE* 3.9 23.5 - - - +
2418B LEU 3.1 18.4 + - - +
2419B ASP* 3.5 9.0 - - - +
2421B ILE* 1.3 77.6 - - - +
2423B ASP* 1.3 59.4 + - - +
2425B MET* 4.8 0.2 - - - -
2426B PHE* 2.9 32.2 + - - +
2427B GLY* 3.1 7.2 + - - -
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Residues in contact with ASP2423 (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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2403B TYR* 2.6 39.8 + - - +
2419B ASP* 2.8 24.1 + - - +
2420B LEU 3.7 3.4 - - - +
2421B ILE 3.3 0.2 - - - -
2422B ALA* 1.3 74.9 - - - +
2424B VAL* 1.3 61.7 + - - +
2427B GLY* 3.5 5.5 + - - +
2428B VAL* 2.8 39.0 + - + +
2429B PRO* 3.4 1.0 - - - +
2540B LYS* 2.7 34.9 + - - -
2543B GLU* 3.4 15.3 - - + +
2547B TRP* 4.2 5.2 - - - +
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Residues in contact with VAL2424 (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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2251B LEU 5.3 0.2 - - - +
2252B THR* 5.7 0.3 - - - -
2253B SER* 5.7 3.1 + - - +
2388B LEU 4.8 0.2 - - - +
2389B VAL* 3.7 43.1 - - + +
2391B ILE* 4.5 1.1 - - + -
2420B LEU* 3.2 21.4 + - + +
2421B ILE 3.8 3.1 - - - +
2423B ASP* 1.3 78.2 - - - +
2425B MET* 1.3 58.9 + - - +
2428B VAL* 5.0 2.9 - - - -
2429B PRO* 3.2 22.1 - - - +
2547B TRP* 3.4 44.2 - - + -
2551B PHE* 4.1 15.1 - - + -
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Residues in contact with MET2425 (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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2B COA 4.1 16.4 - - - -
2252B THR* 3.1 33.0 + - + +
2253B SER 6.0 0.7 - - - +
2254B VAL* 4.0 21.3 - - + -
2355B PHE* 3.9 18.4 - - + -
2359B ILE* 5.1 0.2 - - + -
2388B LEU* 3.6 46.7 - - + +
2389B VAL* 4.4 2.7 - - + -
2421B ILE* 3.0 39.7 + - + +
2424B VAL* 1.3 79.0 - - - +
2426B PHE* 1.3 81.9 + - + +
2429B PRO* 3.6 7.4 - - - +
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Residues in contact with PHE2426 (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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2B COA 5.0 6.3 - - + -
2221B SER* 4.7 4.9 - - - -
2247B SER* 3.4 34.5 - - - -
2248B GLY* 4.1 5.8 - - - -
2252B THR* 4.3 14.8 - - + -
2255B LEU* 6.2 1.1 - - + -
2350B ILE* 4.1 8.7 - - + -
2354B GLU* 3.5 37.0 - - + -
2355B PHE* 5.2 1.3 - + - -
2359B ILE* 3.6 32.1 - - + -
2422B ALA* 2.9 12.0 + - - +
2424B VAL 3.6 0.2 - - - -
2425B MET* 1.3 111.5 - - + +
2427B GLY* 1.3 64.9 + - - +
2428B VAL 3.5 2.0 - - - -
2429B PRO* 3.5 2.8 - - - +
2430B SER* 2.9 33.1 + - - +
2468B HIS* 3.9 10.5 - + - -
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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