Contacts of the helix formed by residues 2292 - 2307 (chain D) in PDB entry 6X34
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 GLN2292 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2290D ALA 4.0 3.5 + - - +
2291D LEU* 1.3 82.9 - - + +
2293D GLU* 1.3 63.3 + - - +
2294D GLN* 3.3 12.4 + - + +
2295D ASP* 4.2 3.9 + - + +
2296D LEU* 3.2 24.5 + - - +
3868D LYS* 3.2 34.4 - - - +
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Residues in contact with GLU2293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291D LEU 4.1 0.4 + - - -
2292D GLN* 1.3 76.0 + - - +
2294D GLN* 1.3 59.1 + - - +
2295D ASP 3.5 0.4 - - - -
2296D LEU* 3.5 12.8 - - + +
2297D GLU* 2.9 30.0 + - - +
2353D VAL* 5.2 17.3 - - + -
2357D LEU* 4.3 10.1 - - + +
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Residues in contact with GLN2294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292D GLN* 3.3 8.9 - - + +
2293D GLU* 1.3 74.9 - - - +
2295D ASP* 1.3 61.3 + - - +
2297D GLU* 3.3 6.2 + - - +
2298D LYS* 2.9 27.9 + - - +
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Residues in contact with ASP2295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255D LEU* 4.7 21.1 - - + +
2256D SER* 5.5 5.8 - - - -
2259D LEU* 4.5 19.9 - - + +
2291D LEU* 5.2 1.8 - - + -
2292D GLN* 4.2 8.0 + - + +
2294D GLN* 1.3 78.7 - - - +
2296D LEU* 1.3 61.2 + - + +
2298D LYS* 3.3 7.9 + - - +
2299D VAL* 2.9 31.8 + - - +
2335D PHE* 4.9 8.1 - - + -
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Residues in contact with LEU2296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291D LEU* 3.7 28.7 - - + -
2292D GLN 3.2 24.5 - - - +
2293D GLU* 3.4 13.0 + - + +
2294D GLN 3.2 0.6 - - - -
2295D ASP* 1.3 80.1 - - + +
2297D GLU* 1.3 62.2 + - - +
2299D VAL* 3.1 4.5 - - + +
2300D VAL* 3.0 30.4 + - + +
2335D PHE* 5.0 8.7 - - + -
2336D LEU* 3.5 29.6 - - + -
2339D ALA* 5.2 5.6 - - + -
2353D VAL* 5.4 6.3 - - + -
2354D VAL* 3.8 22.7 - - + -
2357D LEU* 4.0 15.0 - - + -
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Residues in contact with GLU2297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2293D GLU 2.9 17.8 + - - +
2294D GLN* 3.7 6.5 - - - +
2296D LEU* 1.3 76.0 - - - +
2298D LYS* 1.3 54.6 + - - +
2300D VAL* 3.1 10.4 - - + +
2301D SER* 2.5 40.3 + - - +
2357D LEU* 3.7 15.4 - - + +
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Residues in contact with LYS2298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259D LEU* 5.5 6.5 - - + -
2294D GLN 2.9 17.2 + - - +
2295D ASP* 3.6 9.0 - - - +
2296D LEU 3.2 0.2 - - - -
2297D GLU* 1.3 76.7 - - - +
2299D VAL* 1.3 57.4 + - - +
2301D SER* 3.3 6.2 + - - -
2302D TYR* 2.9 52.0 + - + +
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Residues in contact with VAL2299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259D LEU* 6.1 3.6 - - + -
2295D ASP 2.9 16.7 + - - +
2296D LEU* 3.1 17.9 - - - +
2298D LYS* 1.3 76.1 - - - +
2300D VAL* 1.3 58.5 + - + +
2302D TYR* 3.3 12.1 + - + +
2303D LEU* 2.9 27.9 + - - +
2332D TYR* 4.2 21.2 - - + +
2335D PHE* 3.7 29.2 - - + -
2336D LEU* 3.8 27.6 - - + -
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Residues in contact with VAL2300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296D LEU* 3.0 19.2 + - + +
2297D GLU* 3.1 22.0 - - - +
2299D VAL* 1.3 74.8 - - + +
2301D SER* 1.3 62.6 + - - +
2303D LEU* 3.3 7.2 + - - +
2304D ALA* 2.9 29.5 + - - +
2336D LEU* 3.9 29.2 - - + -
2354D VAL* 5.5 4.3 - - - +
2357D LEU* 4.0 35.2 - - + +
2358D LEU* 5.0 10.8 - - + +
2364D CYS* 5.0 6.0 - - + +
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Residues in contact with SER2301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2297D GLU* 2.5 26.4 + - - +
2298D LYS* 3.6 6.4 - - - -
2300D VAL* 1.3 81.6 - - - +
2302D TYR* 1.3 62.1 + - - +
2304D ALA* 3.3 6.6 + - - +
2305D GLY* 2.9 26.0 + - - -
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Residues in contact with TYR2302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259D LEU* 3.7 21.9 + - + -
2260D GLU* 4.4 13.2 + - - +
2262D SER* 5.2 0.4 - - - -
2263D GLY* 3.3 41.1 - - - +
2298D LYS* 2.9 39.2 + - + +
2299D VAL* 3.7 11.4 - - + +
2300D VAL 3.3 0.2 - - - -
2301D SER* 1.3 82.0 - - - +
2303D LEU* 1.3 56.4 + - - +
2305D GLY* 3.3 1.8 + - - -
2306D CYS* 2.9 30.2 + - - +
2332D TYR* 5.4 3.6 - - + -
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Residues in contact with LEU2303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2299D VAL 2.9 17.6 + - - +
2300D VAL* 3.7 7.6 - - - +
2301D SER 3.3 0.2 - - - -
2302D TYR* 1.3 76.5 - - - +
2304D ALA* 1.3 63.4 + - - +
2306D CYS* 3.5 11.0 + - - +
2307D GLY* 3.7 8.1 + - - -
2329D GLY* 6.0 2.2 - - - -
2332D TYR* 4.1 25.9 - - + +
2333D LEU* 5.1 15.0 - - + -
2336D LEU* 6.0 3.1 - - + -
2363D GLU 5.4 0.3 - - - +
2364D CYS* 5.0 9.7 - - + +
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Residues in contact with ALA2304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300D VAL 2.9 17.2 + - - +
2301D SER* 3.7 7.2 - - - +
2302D TYR 3.3 0.2 - - - -
2303D LEU* 1.3 79.0 - - - +
2305D GLY* 1.3 60.5 + - - +
2306D CYS 3.4 0.2 + - - -
2307D GLY* 3.7 2.3 + - - -
2308D LEU* 3.4 20.8 + - - +
2361D LYS* 5.0 10.3 - - + -
2363D GLU* 4.3 15.3 - - + +
2364D CYS* 4.1 30.0 - - + +
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Residues in contact with GLY2305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2301D SER 2.9 16.4 + - - -
2302D TYR* 3.7 2.2 - - - -
2304D ALA* 1.3 74.9 - - - +
2306D CYS* 1.3 63.9 + - - +
2308D LEU* 3.6 17.8 + - - +
2309D GLN* 4.3 3.6 + - - +
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Residues in contact with CYS2306 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2302D TYR 2.9 17.7 + - - +
2303D LEU* 3.7 9.2 - - - +
2304D ALA 3.2 0.6 - - - -
2305D GLY* 1.3 79.6 - - - +
2307D GLY* 1.3 58.0 + - - +
2308D LEU 3.3 0.2 - - - -
2309D GLN 3.3 18.2 - - - +
2310D SER 5.5 0.2 - - - -
2311D CYS* 5.6 2.3 - - - +
2325D ASN* 3.8 32.0 + - - +
2328D GLY* 4.1 9.2 - - - +
2329D GLY* 4.0 22.9 - - - -
2332D TYR* 5.8 2.2 - - + -
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Residues in contact with GLY2307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303D LEU 3.7 6.1 + - - -
2304D ALA 3.7 6.3 + - - -
2305D GLY 3.5 0.2 - - - -
2306D CYS* 1.3 79.2 - - - +
2308D LEU* 1.3 62.3 + - - +
2309D GLN 3.4 1.6 - - - -
2323D GLY 4.9 0.2 - - - -
2324D TRP* 3.6 36.3 + - - +
2325D ASN 4.4 1.8 - - - -
2363D GLU 5.5 5.6 - - - +
2367D PRO* 6.0 1.2 - - - +
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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