Contacts of the helix formed by residues 2329 - 2349 (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 SER2329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2328A PRO* 1.3 80.4 - - - +
2330A LEU* 1.3 56.1 + - - +
2332A LEU* 2.7 33.8 + - - +
2333A THR* 2.8 11.8 + - - -
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Residues in contact with LEU2330 (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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2328A PRO 3.6 12.9 - - - -
2329A SER* 1.3 77.0 - - - +
2331A LYS* 1.3 62.4 + - - +
2333A THR* 3.1 12.7 - - - +
2334A TYR* 3.0 15.9 + - - +
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Residues in contact with LYS2331 (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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2323A CYS* 5.1 20.6 - - + +
2328A PRO* 2.6 22.4 + - + +
2330A LEU* 1.3 72.4 - - - +
2332A LEU* 1.3 49.8 - - - +
2334A TYR* 2.6 14.8 + - + +
2335A THR* 2.1 41.1 + - - -
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Residues in contact with LEU2332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2328A PRO 3.1 5.4 + - - +
2329A SER* 2.7 31.0 + - - +
2331A LYS* 1.3 70.9 - - - +
2333A THR* 1.3 48.2 + - - -
2335A THR* 2.9 12.5 - - - -
2336A GLU* 2.1 38.2 + - - +
2369A GLY* 4.4 19.7 - - - +
2370A ASN* 6.0 0.4 - - - -
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Residues in contact with THR2333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2329A SER 2.8 9.1 + - - -
2330A LEU* 3.1 13.2 - - - -
2332A LEU* 1.3 73.1 - - - +
2334A TYR* 1.3 51.8 - - - +
2336A GLU* 2.7 11.3 + - - +
2337A CYS* 2.1 39.9 + - - +
2378A GLU* 6.6 0.2 - - - -
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Residues in contact with TYR2334 (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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2288A VAL 5.3 9.0 - - - +
2290A GLU* 5.9 7.6 - - + -
2319A LEU* 5.3 13.8 - - + +
2330A LEU 3.0 7.7 + - - +
2331A LYS* 2.6 25.6 + - + +
2333A THR* 1.3 71.4 - - - +
2335A THR* 1.3 47.5 - - - -
2337A CYS* 2.9 12.4 + - + +
2338A LEU* 2.2 38.1 + - - +
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Residues in contact with THR2335 (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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2331A LYS 2.1 26.8 + - - -
2332A LEU* 3.1 17.3 - - - -
2334A TYR* 1.3 65.8 - - - +
2336A GLU* 1.3 50.7 + - - +
2338A LEU* 2.8 13.0 + - - +
2339A ARG* 2.2 35.3 + - - -
2366A GLU* 3.4 25.4 - - - +
2369A GLY* 4.7 7.2 - - - -
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Residues in contact with GLU2336 (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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2332A LEU 2.1 29.1 + - - +
2333A THR* 2.7 17.5 + - - +
2335A THR* 1.3 67.2 - - - +
2337A CYS* 1.3 48.8 + - - +
2339A ARG* 2.9 12.5 + - + +
2340A VAL* 2.5 34.9 + - - +
2366A GLU 5.4 1.1 + - - -
2382A GLY* 4.8 18.8 - - - -
2385A LYS* 5.6 5.0 - - + +
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Residues in contact with CYS2337 (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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2290A GLU* 6.6 0.2 - - - -
2293A LEU* 5.1 15.7 - - + -
2316A ILE* 6.1 0.2 - - - -
2333A THR 2.1 26.8 + - - +
2334A TYR* 2.9 18.8 - - + +
2336A GLU* 1.3 66.7 - - - +
2338A LEU* 1.3 48.0 + - - +
2340A VAL* 2.6 12.7 + - + +
2341A CYS* 2.3 38.0 + - - +
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Residues in contact with LEU2338 (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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2316A ILE* 4.9 16.1 - - + +
2319A LEU* 6.4 1.3 - - + -
2320A ASP* 5.6 8.3 - - + +
2334A TYR 2.2 28.2 + - - +
2335A THR* 2.8 17.2 + - - +
2337A CYS* 1.3 66.6 - - - +
2339A ARG* 1.3 57.4 + - - +
2341A CYS* 2.9 25.3 - - + +
2342A GLY 3.0 5.7 + - - -
2362A GLU 5.6 0.5 - - - -
2363A LYS* 5.0 3.5 + - - -
2366A GLU* 4.1 9.6 - - + +
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Residues in contact with ARG2339 (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 2.2 24.6 + - - +
2336A GLU* 2.9 18.4 + - - +
2338A LEU* 1.3 65.6 - - - +
2340A VAL* 1.3 54.5 + - - +
2341A CYS 2.9 1.3 - - - -
2342A GLY* 2.4 26.4 + - - +
2343A ASN* 2.7 9.5 + - - +
2363A LYS* 4.6 11.8 - - + +
2366A GLU* 3.7 18.6 - - + +
2385A LYS* 4.8 15.3 - - + +
2386A ALA* 5.2 9.6 - - + -
2389A SER* 6.1 3.0 - - - -
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Residues in contact with VAL2340 (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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2336A GLU 2.5 15.8 + - - +
2337A CYS* 2.6 15.1 + - + +
2339A ARG* 1.3 72.2 - - - +
2341A CYS* 1.3 47.1 - - - -
2343A ASN* 2.9 13.4 + - + +
2344A TRP* 2.1 38.9 + - - +
2385A LYS 5.8 0.4 + - - -
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Residues in contact with CYS2341 (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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2313A LYS* 5.4 8.1 - - + -
2316A ILE* 4.4 17.9 - - + -
2337A CYS 2.3 24.7 + - - +
2338A LEU* 2.9 23.3 - - - +
2340A VAL* 1.3 68.6 - - - +
2342A GLY* 1.3 47.6 + - - +
2344A TRP* 2.6 10.7 + - + +
2345A LEU* 2.0 41.6 + - - +
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Residues in contact with GLY2342 (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 3.0 8.4 + - - -
2339A ARG 2.4 14.3 + - - -
2341A CYS* 1.3 70.0 - - - +
2343A ASN* 1.3 49.9 + - - -
2345A LEU* 2.9 11.9 + - - +
2346A ALA* 2.3 36.5 + - - +
2359A THR* 4.9 8.7 - - - -
2360A TYR* 5.5 0.9 - - - -
2363A LYS* 4.5 15.5 - - - -
2393A PHE* 6.2 4.0 - - - -
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Residues in contact with ASN2343 (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 2.7 9.6 + - - +
2340A VAL* 3.1 22.0 - - + +
2342A GLY* 1.3 71.0 - - - -
2344A TRP* 1.3 48.5 - - - +
2346A ALA* 2.9 13.5 - - + +
2347A GLU* 2.1 34.7 + - - +
2389A SER* 5.6 10.2 - - - -
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Residues in contact with TRP2344 (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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2296A ALA* 6.2 5.8 - - + -
2309A LEU* 5.6 11.0 - - + +
2340A VAL 2.1 28.6 + - - +
2341A CYS* 2.6 17.9 + - - +
2343A ASN* 1.3 66.3 - - - +
2345A LEU* 1.3 52.4 + - - -
2347A GLU* 2.9 15.2 - - + +
2348A THR* 2.6 31.7 + - - -
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Residues in contact with LEU2345 (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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2341A CYS 2.0 27.2 + - - +
2342A GLY* 3.1 17.5 - - - +
2344A TRP* 1.3 66.6 - - - +
2346A ALA* 1.3 48.0 - - - +
2348A THR* 3.0 11.8 + - - +
2349A CYS* 2.2 33.1 + - - -
2350A LEU 3.6 1.2 + - - -
2351A GLU* 4.6 13.0 + - + -
2359A THR* 4.3 19.1 - - - -
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Residues in contact with ALA2346 (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 2.3 26.5 + - - +
2343A ASN* 3.0 17.0 - - + +
2345A LEU* 1.3 63.7 - - - +
2347A GLU* 1.3 56.3 + - - +
2348A THR 2.9 1.6 - - - -
2349A CYS* 2.4 39.9 + - + +
2393A PHE* 5.7 9.6 - - + -
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Residues in contact with GLU2347 (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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2299A PHE* 4.8 16.6 - - + -
2305A GLN* 5.7 2.5 - - - -
2343A ASN 2.1 21.2 + - - +
2344A TRP* 2.7 28.5 + - + +
2346A ALA* 1.3 66.4 - - - +
2348A THR* 1.3 59.8 + - - +
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Residues in contact with THR2348 (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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2305A GLN* 5.3 13.9 - - - +
2344A TRP 2.6 13.1 + - - -
2345A LEU* 3.0 15.0 - - - -
2346A ALA 2.9 4.2 - - - +
2347A GLU* 1.3 72.6 - - - +
2349A CYS* 1.3 65.5 + - - +
2350A LEU* 3.4 23.5 - - - +
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Residues in contact with CYS2349 (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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2345A LEU 2.2 24.4 + - - -
2346A ALA* 2.4 27.5 + - + +
2348A THR* 1.3 67.7 - - - +
2350A LEU* 1.3 58.9 - - - +
2351A GLU* 3.4 6.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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