Contacts of the helix formed by residues 2358 - 2368 (chain A) in PDB entry 5NP1
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 GLN2358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2354A ALA 2.0 24.0 + - - +
2355A VAL* 3.0 14.8 - - + +
2356A ILE 2.8 4.2 - - - -
2357A MET* 1.3 68.3 - - - +
2359A THR* 1.3 52.6 - - - +
2361A LEU* 3.0 2.9 - - - +
2362A GLU* 2.1 40.6 + - - +
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Residues in contact with THR2359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2342A GLY* 4.9 5.4 - - - -
2345A LEU* 4.3 24.2 - - - -
2351A GLU* 4.7 5.2 - - - -
2355A VAL* 2.0 32.1 + - - -
2356A ILE* 2.8 1.3 + - - -
2358A GLN* 1.3 66.7 - - - +
2360A TYR* 1.3 53.3 + - - -
2362A GLU* 2.9 10.4 + - - +
2363A LYS* 2.1 37.9 + - - +
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Residues in contact with TYR2360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2342A GLY* 5.5 1.7 - - - -
2356A ILE* 2.4 41.4 + - + +
2357A MET* 5.2 0.2 - - - -
2359A THR* 1.3 73.3 - - - +
2361A LEU* 1.3 47.9 - - - -
2363A LYS* 3.0 12.2 - - + +
2364A ALA* 2.1 36.6 + - - +
2393A PHE* 4.6 20.2 - - + -
2394A SER* 5.6 2.5 - - - +
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Residues in contact with LEU2361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2356A ILE 2.3 21.2 + - - -
2357A MET* 2.8 33.1 - - - +
2358A GLN* 3.1 2.5 - - - +
2360A TYR* 1.3 65.2 - - - +
2362A GLU* 1.3 54.3 + - - +
2364A ALA* 3.0 11.3 - - + +
2365A VAL* 2.2 39.9 + - - +
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Residues in contact with GLU2362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2338A LEU 5.6 1.1 - - - -
2358A GLN 2.1 29.5 + - - +
2359A THR* 3.0 16.8 - - - +
2361A LEU* 1.3 65.7 - - - +
2363A LYS* 1.3 49.0 + - - +
2365A VAL* 3.1 10.3 + - - +
2366A GLU* 2.2 36.0 + - - +
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Residues in contact with LYS2363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2338A LEU 5.0 1.9 + - - -
2339A ARG* 4.6 12.3 - - + +
2342A GLY* 4.5 16.4 - - - -
2359A THR 2.1 27.7 + - - +
2360A TYR* 3.1 18.6 - - + +
2362A GLU* 1.3 66.0 - - - +
2364A ALA* 1.3 50.7 - - - +
2366A GLU* 2.7 9.9 + - - +
2367A VAL* 2.0 40.8 + - - +
2390A LEU* 6.6 0.4 - - - -
2393A PHE* 6.1 2.5 - - + -
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Residues in contact with ALA2364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2360A TYR 2.1 27.3 + - - +
2361A LEU* 2.7 18.1 + - + +
2363A LYS* 1.3 67.7 - - - +
2365A VAL* 1.3 47.3 - - - -
2367A VAL* 2.9 13.0 - - + +
2368A ALA* 2.2 34.9 + - - +
2390A LEU* 6.3 1.3 - - - -
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Residues in contact with VAL2365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2361A LEU 2.2 26.6 + - - +
2362A GLU* 3.2 14.1 - - - +
2364A ALA* 1.3 65.8 - - - +
2366A GLU* 1.3 53.1 + - - +
2368A ALA* 2.6 13.6 + - + +
2369A GLY* 2.4 32.6 + - - -
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Residues in contact with GLU2366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2335A THR* 3.4 35.4 - - - +
2336A GLU* 5.4 0.9 + - - -
2338A LEU* 4.1 7.2 - - + -
2339A ARG* 3.7 16.6 - - + +
2362A GLU 2.2 29.0 + - - +
2363A LYS* 2.7 16.2 + - - +
2365A VAL* 1.3 67.2 - - - +
2367A VAL* 1.3 52.5 + - - +
2369A GLY* 2.6 26.4 + - - +
2370A ASN 4.0 0.5 + - - -
2386A ALA* 5.5 0.8 - - - +
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Residues in contact with VAL2367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2339A ARG* 5.3 0.4 - - - +
2363A LYS 2.0 27.4 + - - +
2364A ALA* 2.9 18.2 - - + +
2366A GLU* 1.3 67.9 - - - +
2368A ALA* 1.3 59.7 + - - +
2369A GLY 3.2 0.7 + - - -
2370A ASN* 3.4 17.7 + - - +
2386A ALA* 4.2 26.2 - - + +
2387A PHE* 6.2 0.2 - - - -
2390A LEU* 4.9 12.6 - - + -
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Residues in contact with ALA2368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2364A ALA 2.2 25.5 + - - +
2365A VAL* 2.6 19.3 + - + +
2367A VAL* 1.3 66.3 - - - +
2369A GLY* 1.3 63.1 + - - -
2370A ASN 2.8 16.4 - - - +
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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