Contacts of the helix formed by residues 2374 - 2385 (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 ASP2374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2373B LEU* 1.3 77.4 - - - +
2375B GLN* 1.3 66.6 + - - +
2376B LYS* 3.4 13.4 - - + +
2377B THR* 2.6 46.9 + - - -
2378B ALA* 3.0 20.1 + - - +
2404B LEU* 5.2 0.2 - - - -
2410B THR* 4.5 10.3 - - + +
2413B LYS* 4.6 4.0 - - - +
4461D PRO* 4.1 5.2 - - - +
4462D LYS* 3.5 35.4 + - + +
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Residues in contact with GLN2375 (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 4.1 0.4 + - - -
2374B ASP* 1.3 70.0 - - - +
2376B LYS* 1.3 67.1 + - - +
2378B ALA* 3.0 8.9 + - - +
2379B MET* 2.9 37.1 + - + +
2400B THR* 4.2 9.7 - - + +
2401B GLU* 2.9 29.2 + - - +
2404B LEU* 4.1 17.3 - - + -
2405B GLY* 3.3 22.6 + - - -
2413B LYS* 3.1 33.9 + - + +
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Residues in contact with LYS2376 (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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2374B ASP* 3.3 10.9 + - + +
2375B GLN* 1.3 80.1 - - - +
2377B THR* 1.3 64.0 + - - +
2379B MET* 3.4 19.9 + - + +
2380B SER* 3.3 24.7 + - - +
4458D ASP* 5.8 4.5 - - - +
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Residues in contact with THR2377 (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* 3.5 19.3 - - + -
2374B ASP* 2.6 43.2 + - - -
2375B GLN 3.2 0.2 - - - -
2376B LYS* 1.3 75.8 - - - +
2378B ALA* 1.3 63.6 + - - +
2380B SER* 3.2 4.0 + - - -
2381B LEU* 2.9 26.7 + - + +
4458D ASP 3.9 16.2 + - - +
4459D MET 3.5 25.8 - - - +
4460D LYS 4.0 3.8 + - - -
4461D PRO* 3.8 16.0 - - + +
4462D LYS 4.2 1.0 + - - -
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Residues in contact with ALA2378 (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* 3.9 10.7 - - + +
2374B ASP 3.0 13.9 + - - +
2375B GLN* 3.3 9.0 - - - +
2377B THR* 1.3 76.9 - - - +
2379B MET* 1.3 56.9 + - - +
2381B LEU* 3.1 3.6 + - - +
2382B LEU* 2.8 30.9 + - - +
2400B THR* 4.0 7.4 - - + -
2404B LEU* 3.8 26.5 - - + -
2417B PHE* 3.5 22.8 - - + -
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Residues in contact with MET2379 (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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2375B GLN* 2.9 22.1 + - + +
2376B LYS* 3.7 26.0 - - + +
2377B THR 3.3 0.2 - - - -
2378B ALA* 1.3 75.5 - - - +
2380B SER* 1.3 62.7 + - - +
2382B LEU 3.3 0.3 + - - -
2383B TRP* 3.0 23.6 + - - +
2396B ILE* 3.6 22.2 - - + +
2397B PRO* 4.0 34.5 - - - -
2400B THR* 3.7 20.4 - - + +
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Residues in contact with SER2380 (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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2376B LYS* 3.3 13.8 + - - +
2377B THR 3.2 8.8 + - - -
2379B MET* 1.3 77.3 - - - +
2381B LEU* 1.3 62.7 + - - +
2383B TRP* 3.3 8.4 + - - +
2384B LYS* 3.2 27.1 + - - +
4458D ASP* 3.3 41.6 + - - +
4459D MET* 4.5 4.0 - - - -
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Residues in contact with LEU2381 (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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2306B LEU* 6.1 0.4 - - + -
2366B TYR* 3.8 7.3 + - + +
2367B PRO* 3.5 39.7 - - + +
2368B LEU* 3.4 33.4 - - + -
2373B LEU* 4.0 19.1 - - + -
2377B THR* 2.9 20.2 + - + +
2378B ALA 3.1 6.5 + - - +
2380B SER* 1.3 78.0 - - - +
2382B LEU* 1.3 56.8 + - - +
2384B LYS* 3.2 7.2 + - + +
2385B SER* 2.8 33.1 + - - -
2417B PHE* 3.8 17.3 - - + -
4459D MET* 4.0 19.1 - - + +
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Residues in contact with LEU2382 (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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2378B ALA 2.8 20.3 + - - +
2379B MET 3.7 5.2 - - - +
2381B LEU* 1.3 73.8 - - - +
2383B TRP* 1.3 62.3 + - - +
2385B SER* 3.2 15.6 + - - -
2386B TYR* 3.5 5.2 + - - -
2389B VAL* 4.1 7.3 - - + +
2391B ILE* 4.0 27.3 - - + +
2396B ILE* 3.9 27.0 - - + +
2399B ALA* 4.2 13.2 - - + -
2400B THR* 3.7 20.4 - - - +
2417B PHE* 4.0 12.5 - - + -
2420B LEU* 4.2 13.7 - - + -
2421B ILE* 3.6 29.8 - - + -
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Residues in contact with TRP2383 (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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2311B ASP* 4.1 2.0 - - - -
2312B PRO* 3.2 49.9 - - + +
2313B ARG* 3.7 38.6 - - + -
2379B MET 3.0 13.8 + - - +
2380B SER* 3.6 11.4 - - - +
2381B LEU 3.2 0.2 - - - -
2382B LEU* 1.3 77.0 - - - +
2384B LYS* 1.3 69.5 + - + +
2386B TYR* 3.0 35.2 + + - +
2391B ILE 4.1 6.3 - - - -
2393B LYS* 3.6 74.9 - - + +
2396B ILE* 4.3 8.9 - - + +
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Residues in contact with LYS2384 (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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2306B LEU* 3.4 27.7 - - + +
2307B ASP 4.4 7.7 + - - +
2308B LEU* 3.3 41.4 + - + +
2309B GLN 4.2 0.2 - - - -
2310B GLY 3.2 27.9 + - - +
2312B PRO* 4.0 17.3 - - + +
2315B SER* 5.3 0.2 + - - -
2380B SER 3.2 13.2 + - - +
2381B LEU* 3.6 11.4 - - + +
2383B TRP* 1.3 85.0 - - + +
2385B SER* 1.3 56.9 + - - +
2386B TYR 3.1 3.4 + - - -
2387B PRO* 3.5 7.7 - - - +
4459D MET* 4.1 27.4 - - + -
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Residues in contact with SER2385 (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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2306B LEU* 4.3 7.6 - - - +
2366B TYR* 2.6 39.1 + - - -
2381B LEU 2.8 15.1 + - - -
2382B LEU* 3.5 12.3 - - - -
2383B TRP 3.1 1.0 - - - -
2384B LYS* 1.3 75.5 - - - +
2386B TYR* 1.3 53.8 + - - +
2387B PRO* 3.2 5.4 - - - -
2388B LEU* 2.7 34.3 + - - +
2389B VAL* 3.1 17.5 + - - -
2421B ILE* 4.4 8.5 - - - -
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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