Contacts of the helix formed by residues 2423 - 2437 (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 ILE2423 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2322D ILE* 4.1 17.7 - - + -
2324D TRP* 3.5 37.5 - - + -
2326D PRO* 5.1 4.7 - - + -
2380D THR* 5.0 9.0 - - + -
2381D ILE* 5.2 1.6 - - + -
2384D ALA* 4.4 22.7 - - + -
2422D ALA* 1.3 88.3 - - + +
2424D MET* 1.3 62.4 + - - +
2426D PHE* 3.3 2.1 + - - +
2427D TYR* 2.9 48.9 + - + -
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Residues in contact with MET2424 (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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2381D ILE* 4.8 9.0 - - + -
2384D ALA* 5.1 3.4 - - + +
2385D ILE* 3.8 30.1 - - + -
2422D ALA 4.5 1.5 - - - +
2423D ILE* 1.3 80.4 - - - +
2425D SER* 1.3 58.6 + - - +
2427D TYR* 3.4 5.8 + - - +
2428D ALA 2.9 24.3 + - - -
2495D PHE* 5.5 1.1 - - + -
2499D HIS* 3.1 29.2 - - + +
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Residues in contact with SER2425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330D GLU* 5.7 4.3 - - - -
2422D ALA* 3.6 22.5 + - - +
2423D ILE 3.3 0.4 - - - -
2424D MET* 1.3 77.6 - - - +
2426D PHE* 1.3 57.7 + - - +
2428D ALA* 3.3 3.4 + - - +
2429D ALA* 2.9 29.5 + - - +
2499D HIS* 3.2 19.6 + - - -
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Residues in contact with PHE2426 (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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2324D TRP* 3.4 39.7 - + + -
2325D ASN 4.9 0.9 - - - -
2326D PRO 4.0 9.2 - - - +
2329D GLY* 3.6 37.2 - - - -
2330D GLU* 3.9 6.5 - - - +
2333D LEU* 3.6 21.3 - - + -
2364D CYS 5.0 10.1 - - - -
2365D PHE 5.6 0.2 - - - -
2366D GLY* 4.9 12.6 - - - -
2367D PRO* 5.8 0.4 - - + -
2422D ALA 3.0 19.6 + - - +
2423D ILE 3.7 2.9 - - - +
2425D SER* 1.3 76.2 - - - +
2427D TYR* 1.3 66.6 + + - +
2429D ALA* 3.3 5.9 + - - +
2430D LEU* 2.9 46.3 + - + +
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Residues in contact with TYR2427 (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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2324D TRP* 4.0 13.3 + + - -
2366D GLY* 4.1 19.4 - - - -
2367D PRO* 4.2 4.0 - - - +
2368D ALA* 3.4 33.7 + - + +
2369D LEU* 4.9 14.1 - - + -
2377D LEU* 5.1 15.7 - - + -
2380D THR* 4.5 9.5 - - + +
2381D ILE* 3.6 31.0 - - + -
2423D ILE* 2.9 47.2 + - + +
2424D MET 3.8 2.7 - - - +
2426D PHE* 1.3 82.8 - + - +
2428D ALA* 1.3 57.9 + - - +
2430D LEU* 3.3 15.4 + - + +
2431D ILE* 2.9 32.0 + - - +
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Residues in contact with ALA2428 (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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2424D MET 2.9 17.5 + - - +
2425D SER* 3.7 5.2 - - - +
2427D TYR* 1.3 74.1 - - - +
2429D ALA* 1.3 59.0 + - - +
2431D ILE* 3.1 11.6 - - - +
2432D ASP* 2.9 31.3 + - - +
2498D ASP 5.7 0.2 - - - -
2499D HIS* 3.6 31.9 - - + +
2502D SER* 4.2 10.5 - - - -
2503D MET* 5.1 4.9 - - - -
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Residues in contact with ALA2429 (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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2330D GLU* 5.0 10.5 - - + -
2333D LEU* 4.7 14.3 - - + +
2334D ASP* 4.9 12.8 - - - +
2337D ARG* 6.0 0.9 - - - +
2425D SER 2.9 17.8 + - - +
2426D PHE* 3.7 5.8 - - - +
2428D ALA* 1.3 75.2 - - - +
2430D LEU* 1.3 58.1 + - - +
2432D ASP* 3.4 5.8 + - - +
2433D LEU* 2.9 31.0 + - - +
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Residues in contact with LEU2430 (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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2333D LEU* 4.1 31.1 - - + +
2358D LEU* 5.6 3.8 - - + -
2364D CYS* 4.9 7.9 - - - +
2365D PHE* 4.3 16.2 - - + -
2366D GLY* 3.9 25.4 - - - +
2426D PHE* 2.9 29.4 + - + +
2427D TYR* 3.6 15.5 - - + +
2428D ALA 3.3 0.2 - - - -
2429D ALA* 1.3 78.2 - - - +
2431D ILE* 1.3 57.9 + - - +
2433D LEU* 3.3 3.1 + - + +
2434D LEU* 2.9 53.2 + - + +
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Residues in contact with ILE2431 (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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2377D LEU* 6.0 1.1 - - + -
2427D TYR 2.9 18.0 + - - +
2428D ALA* 3.1 22.0 - - - +
2430D LEU* 1.3 74.9 - - - +
2432D ASP* 1.3 59.2 + - - +
2434D LEU* 3.3 6.7 + - + -
2435D GLY 2.9 23.7 + - - -
2462D VAL* 3.7 28.7 - - + -
2502D SER* 5.0 4.0 - - - +
2503D MET* 4.1 28.7 - - + -
2506D PHE* 3.5 50.4 - - + -
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Residues in contact with ASP2432 (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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2337D ARG* 5.3 13.3 - - - +
2341D PHE* 5.5 0.2 - - - -
2428D ALA 2.9 18.3 + - - +
2429D ALA* 3.7 6.7 - - - +
2431D ILE* 1.3 79.4 - - - +
2433D LEU* 1.3 56.2 + - - +
2435D GLY* 3.4 1.9 + - - -
2436D ARG* 2.9 29.5 + - - +
2502D SER* 4.4 20.9 - - - +
2505D LEU* 6.5 2.0 - - + -
2506D PHE* 5.4 2.5 - - - +
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Residues in contact with LEU2433 (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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2333D LEU* 3.3 51.1 - - + +
2336D LEU* 3.5 30.1 - - + +
2337D ARG* 3.9 17.4 - - + +
2340D VAL* 5.4 6.6 - - + +
2354D VAL* 5.9 4.3 - - + -
2358D LEU* 4.6 12.3 - - + -
2429D ALA 2.9 16.5 + - - +
2430D LEU* 3.3 6.0 + - + +
2432D ASP* 1.3 75.5 - - - +
2434D LEU* 1.3 75.8 + - + +
2436D ARG* 3.2 12.9 + - - +
2437D CYS* 3.1 25.0 + - + +
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Residues in contact with LEU2434 (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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2355D VAL* 5.8 2.2 - - + -
2358D LEU* 3.6 33.4 - - + -
2359D ILE* 6.4 0.9 - - + -
2365D PHE* 3.9 17.7 - - + -
2430D LEU* 2.9 45.6 + - + +
2431D ILE* 3.3 15.7 + - + +
2433D LEU* 1.3 79.9 - - + +
2435D GLY* 1.3 58.9 + - - +
2437D CYS* 3.2 23.3 + - - -
2438D ALA* 4.1 6.4 + - - +
2458D LEU* 4.8 20.2 - - + +
2461D LEU* 5.3 11.9 - - + -
2462D VAL* 5.8 5.4 - - + -
2506D PHE* 4.6 4.7 - - + -
2510D VAL* 4.8 1.9 - - - +
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Residues in contact with GLY2435 (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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2431D ILE 2.9 12.2 + - - -
2432D ASP 3.7 2.0 - - - -
2434D LEU* 1.3 76.6 - - - +
2436D ARG* 1.3 55.8 + - - +
2438D ALA* 3.5 12.4 + - - +
2506D PHE* 3.5 28.8 - - - -
2509D ARG* 2.7 32.3 + - - +
2510D VAL* 3.9 7.6 - - - -
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Residues in contact with ARG2436 (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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2337D ARG* 5.1 2.2 - - - -
2340D VAL* 3.9 18.8 - - + +
2341D PHE* 3.5 30.0 - - + -
2346D SER* 3.5 13.2 + - - -
2432D ASP 2.9 18.0 + - - +
2433D LEU* 3.2 8.4 + - - +
2435D GLY* 1.3 72.2 - - - +
2437D CYS* 1.3 57.6 + - - +
2438D ALA 3.1 5.5 + - - +
2509D ARG* 2.8 29.7 + - - +
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Residues in contact with CYS2437 (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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2340D VAL* 4.6 9.8 - - + +
2346D SER* 5.5 0.9 - - - -
2351D ALA* 3.5 25.0 - - + +
2354D VAL* 4.0 18.8 - - + -
2355D VAL* 3.5 34.4 - - + +
2358D LEU* 5.5 2.0 - - - -
2433D LEU* 3.1 25.1 + - - +
2434D LEU* 3.2 25.4 - - - -
2436D ARG* 1.3 76.5 - - - +
2438D ALA* 1.3 62.8 + - - +
2439D PRO* 3.7 4.5 - - - +
2454D ILE* 5.4 1.9 - - - +
2458D LEU* 4.6 2.7 - - - +
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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