Contacts of the helix formed by residues 2449 - 2462 (chain H) 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 GLY2449 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2448H LYS* 1.3 75.9 - - - +
2450H GLU* 1.3 62.1 + - - +
2451H ALA 3.5 1.0 - - - +
2452H LEU* 3.7 23.0 + - - +
2453H ARG* 4.3 5.9 + - - +
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Residues in contact with GLU2450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2448H LYS* 3.0 11.0 + - + +
2449H GLY* 1.3 78.4 - - - +
2451H ALA* 1.3 62.2 + - - +
2452H LEU 3.4 0.7 + - - -
2453H ARG* 3.7 32.8 + - - +
2454H ILE* 4.5 3.1 + - - +
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Residues in contact with ALA2451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2439H PRO* 3.9 24.2 - - + +
2444H ILE* 3.3 30.5 + - + +
2448H LYS* 4.7 1.9 - - + +
2449H GLY 3.5 1.8 - - - +
2450H GLU* 1.3 75.6 - - - +
2452H LEU* 1.3 59.6 + - - +
2453H ARG 3.2 0.9 - - - -
2454H ILE* 3.2 15.5 - - + +
2455H ARG* 2.9 30.5 + - - +
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Residues in contact with LEU2452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2444H ILE 5.2 0.8 + - - -
2449H GLY* 3.7 22.6 + - - +
2450H GLU 3.2 1.4 - - - -
2451H ALA* 1.3 78.5 - - - +
2453H ARG* 1.3 56.4 + - - +
2455H ARG* 3.5 15.0 - - - +
2456H ALA* 2.9 30.7 + - - +
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Residues in contact with ARG2453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F VAL* 3.8 15.9 + - - +
175F SER* 3.3 25.9 + - - +
176F SER* 4.6 2.7 - - - +
177F GLU* 3.9 27.0 - - - +
2449H GLY 4.3 4.7 + - - +
2450H GLU* 3.7 23.6 + - - +
2451H ALA 3.2 1.0 - - - -
2452H LEU* 1.3 79.7 - - - +
2454H ILE* 1.3 71.2 + - + +
2456H ALA* 3.3 5.2 + - - +
2457H ILE* 2.9 40.4 + - + +
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Residues in contact with ILE2454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2348H GLU 5.9 0.9 - - - +
2351H ALA* 5.7 2.0 - - + -
2352H ASN* 5.0 17.0 - - + +
2355H VAL* 4.7 24.9 - - + -
2437H CYS 5.4 3.6 - - - +
2439H PRO* 3.6 27.1 - - + -
2450H GLU 4.8 2.9 - - - +
2451H ALA* 3.2 19.0 - - + +
2453H ARG* 1.3 97.0 - - + +
2455H ARG* 1.3 61.7 + - - +
2457H ILE* 3.5 11.3 - - + +
2458H LEU* 2.9 35.2 + - + +
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Residues in contact with ARG2455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2439H PRO* 3.7 28.0 + - + +
2440H GLU* 5.4 1.8 - - - +
2445H GLN* 3.4 32.2 - - - +
2451H ALA* 2.9 21.2 + - - +
2452H LEU* 3.5 12.8 - - - +
2453H ARG 3.2 0.4 - - - -
2454H ILE* 1.3 77.6 - - - +
2456H ALA* 1.3 59.5 + - - +
2458H LEU* 3.2 17.2 - - + +
2459H ARG* 2.9 31.0 + - + +
2509H ARG 5.4 2.8 + - - -
2510H VAL* 3.6 23.5 + - - +
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Residues in contact with ALA2456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2452H LEU 2.9 16.9 + - - +
2453H ARG* 3.7 5.6 - - - +
2455H ARG* 1.3 77.1 - - - +
2457H ILE* 1.3 64.6 + - + +
2459H ARG* 4.0 5.3 - - - +
2460H SER* 2.9 27.4 + - - -
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Residues in contact with ILE2457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F LEU* 3.7 25.8 - - + -
133F PHE* 5.8 5.4 - - + -
176F SER* 4.2 18.4 - - - +
177F GLU* 6.3 0.7 - - + -
195F PHE* 3.9 15.5 - - + -
2355H VAL* 6.3 2.5 - - + -
2359H ILE* 4.1 33.0 - - + -
2453H ARG* 2.9 28.9 + - + +
2454H ILE* 3.5 12.6 - - + +
2455H ARG 3.2 0.2 - - - -
2456H ALA* 1.3 78.3 - - + +
2458H LEU* 1.3 62.9 + - + +
2460H SER* 2.8 20.0 + - - +
2461H LEU* 3.1 14.5 - - + +
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Residues in contact with LEU2458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2355H VAL* 5.4 10.3 - - + -
2434H LEU* 4.8 21.7 - - + +
2437H CYS 4.6 3.1 - - - +
2438H ALA* 3.7 29.6 - - + +
2439H PRO* 3.8 7.2 - - + -
2454H ILE* 2.9 26.5 + - + +
2455H ARG* 3.2 20.0 - - + +
2457H ILE* 1.3 79.2 - - + +
2459H ARG* 1.3 64.2 + - + +
2460H SER 3.6 0.3 + - - -
2461H LEU* 3.7 18.7 + - - +
2462H VAL* 4.0 6.6 + - - +
2506H PHE* 5.2 6.3 - - + -
2510H VAL* 3.6 37.0 - - + +
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Residues in contact with ARG2459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2455H ARG* 2.9 23.7 + - + +
2456H ALA* 4.0 5.2 - - - +
2458H LEU* 1.3 82.5 - - + +
2460H SER* 1.3 63.7 + - - +
2461H LEU 3.3 0.2 - - - -
2462H VAL 3.4 15.9 - - - +
2463H PRO* 3.8 3.3 - - - +
2506H PHE* 6.1 0.4 - - - -
2510H VAL* 5.7 4.3 - - + +
2511H TYR* 3.1 42.0 + - + +
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Residues in contact with SER2460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS* 4.6 8.0 - - - +
131F LEU* 3.2 29.2 - - - +
133F PHE* 6.2 4.3 - - - -
2456H ALA 2.9 14.7 + - - -
2457H ILE* 2.8 19.4 + - - +
2459H ARG* 1.3 75.5 - - - +
2461H LEU* 1.3 65.7 + - - +
2463H PRO* 4.3 9.5 - - - +
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Residues in contact with LEU2461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS* 5.1 1.6 - - + -
131F LEU* 3.5 30.7 - - + -
2359H ILE* 5.0 9.4 - - + -
2365H PHE* 4.9 28.3 - - + -
2370H ARG* 4.5 21.1 - - + -
2377H LEU* 5.6 2.4 - - - +
2434H LEU* 5.3 9.0 - - + -
2457H ILE* 3.1 31.4 + - + +
2458H LEU* 3.9 11.2 - - - +
2459H ARG 3.3 0.4 - - - -
2460H SER* 1.3 84.9 + - - +
2462H VAL* 1.3 69.2 + - + +
2463H PRO* 3.3 8.5 - - - +
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Residues in contact with VAL2462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377H LEU* 4.3 22.2 - - + -
2431H ILE* 3.7 29.2 - - + -
2434H LEU* 5.8 6.3 - - + -
2458H LEU 4.0 4.6 + - - +
2459H ARG* 3.4 10.0 + - - +
2461H LEU* 1.3 85.8 - - + +
2463H PRO* 1.3 70.1 - - - +
2466H ASP* 3.6 25.6 - - + -
2467H LEU* 4.9 2.0 - - - +
2503H MET* 6.6 0.4 - - + -
2506H PHE* 4.0 23.3 - - + -
2511H TYR* 3.9 10.4 - - - -
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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