Contacts of the helix formed by residues 2426 - 2440 (chain B) in PDB entry 2DQZ
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 PHE2426 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B PLM 4.6 13.7 - - - -
2247B SER* 3.4 36.6 - - - -
2248B GLY* 4.2 4.5 - - - +
2249B VAL* 6.0 0.2 - - - -
2252B THR* 5.1 7.2 - - + -
2350B ILE* 4.1 10.5 - - + -
2354B GLU* 3.8 28.5 - - + -
2359B ILE* 3.7 25.1 - - + -
2422B ALA* 2.8 19.5 + - - +
2425B MET* 1.3 116.0 - - + +
2427B GLY* 1.3 65.7 + - - +
2429B PRO* 3.7 2.5 - - - -
2430B SER* 2.5 32.5 + - - +
2468B HIS* 3.4 16.6 - + - -
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Residues in contact with GLY2427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2350B ILE* 4.2 19.9 - - - +
2354B GLU* 5.7 0.6 - - - +
2422B ALA 3.0 12.1 + - - -
2423B ASP* 3.5 8.9 + - - -
2426B PHE* 1.3 82.9 - - - +
2428B VAL* 1.3 63.6 + - - +
2430B SER* 3.6 1.6 - - - -
2431B VAL* 3.2 25.6 + - - +
2540B LYS* 4.7 11.2 - - - -
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Residues in contact with VAL2428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2423B ASP* 2.6 28.3 + - + +
2424B VAL* 4.8 1.8 - - - -
2427B GLY* 1.3 70.1 - - - -
2429B PRO* 1.3 68.1 - - + +
2431B VAL* 3.2 4.2 + - - +
2432B ILE* 3.0 46.0 + - + +
2540B LYS* 5.2 1.2 - - - +
2543B GLU* 4.1 9.4 - - + +
2544B VAL* 3.7 37.7 - - + +
2547B TRP* 3.6 36.3 - - + -
2548B THR* 4.9 1.8 - - - +
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Residues in contact with PRO2429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2249B VAL* 3.8 19.1 - - + -
2251B LEU* 4.0 26.2 - - + +
2252B THR* 5.0 0.4 - - - -
2253B SER 5.9 0.2 - - - +
2423B ASP 3.4 2.7 - - - +
2424B VAL 3.1 26.9 - - - +
2425B MET 3.6 12.3 - - - +
2426B PHE 3.5 7.2 - - - +
2427B GLY 3.5 3.1 - - - -
2428B VAL* 1.3 95.0 - - + +
2430B SER* 1.3 61.2 + - - +
2432B ILE* 3.2 10.9 + - + +
2433B VAL* 3.0 27.4 + - - +
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Residues in contact with SER2430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248B GLY 4.7 6.2 + - - -
2249B VAL* 4.0 14.8 - - - +
2348B VAL* 3.5 27.6 - - - +
2349B GLY 4.6 1.0 + - - -
2350B ILE* 3.2 25.4 - - - +
2426B PHE* 2.5 27.9 + - - +
2427B GLY 3.6 1.6 - - - -
2429B PRO* 1.3 76.2 - - - +
2431B VAL* 1.3 62.8 + - - +
2433B VAL* 3.5 1.0 + - - +
2434B ALA* 3.0 22.3 + - - +
2446B MET* 3.9 6.7 - - - -
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Residues in contact with VAL2431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2350B ILE* 5.8 0.9 - - + -
2427B GLY 3.2 14.6 + - - +
2428B VAL 3.2 6.6 + - - +
2430B SER* 1.3 73.8 - - - +
2432B ILE* 1.3 61.6 + - - +
2434B ALA* 3.1 4.0 + - - +
2435B ARG* 2.8 42.5 + - - +
2446B MET* 4.0 19.7 - - + -
2520B TYR* 3.5 22.4 - - + +
2539B LEU* 3.5 32.1 - - + +
2540B LYS* 4.1 11.7 - - + -
2544B VAL* 4.0 14.6 - - + -
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Residues in contact with ILE2432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251B LEU* 3.5 20.9 - - + -
2336B GLN* 4.3 1.1 - - - +
2428B VAL* 3.0 41.2 + - + +
2429B PRO* 3.2 10.5 + - + +
2431B VAL* 1.3 76.3 - - - +
2433B VAL* 1.3 64.0 + - - +
2435B ARG* 3.0 20.4 + - - +
2436B ASN* 2.8 37.0 + - - +
2544B VAL* 4.4 13.0 - - + -
2548B THR* 5.0 5.4 - - - +
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Residues in contact with VAL2433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2228B SER* 4.5 8.5 - - - +
2249B VAL* 3.8 27.6 - - + -
2250B ALA* 5.6 0.9 - - + -
2251B LEU* 3.7 26.2 - - + +
2336B GLN* 4.1 12.3 - - - +
2346B TYR* 3.9 28.7 - - + -
2348B VAL* 4.5 2.7 - - + -
2429B PRO 3.0 19.2 + - - +
2430B SER 3.8 4.3 - - - +
2432B ILE* 1.3 74.9 - - - +
2434B ALA* 1.3 57.9 + - - +
2436B ASN* 3.5 6.9 + - - +
2437B HIS* 3.0 28.4 + - + +
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Residues in contact with ALA2434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2348B VAL* 4.5 7.6 - - + -
2430B SER 3.0 10.3 + - - +
2431B VAL 3.1 9.4 + - - +
2433B VAL* 1.3 78.2 - - - +
2435B ARG* 1.3 57.6 + - - +
2437B HIS* 3.5 0.8 + - - -
2438B ARG* 3.1 27.4 + - - +
2444B THR* 3.4 19.9 - - + +
2446B MET* 3.3 39.0 - - + -
2520B TYR* 3.9 7.9 - - + -
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Residues in contact with ARG2435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431B VAL* 2.8 28.4 + - - +
2432B ILE* 3.0 10.7 + - - +
2434B ALA* 1.3 74.1 - - - +
2436B ASN* 1.3 62.0 + - - +
2438B ARG* 3.1 23.8 + - - +
2439B ASP* 2.8 37.8 + - - +
2520B TYR* 3.5 19.8 + - + +
2524B GLU* 2.8 32.6 + - - -
2539B LEU 5.3 0.2 + - - -
2541B ASP* 3.2 33.7 + - - +
2544B VAL* 3.5 28.3 - - - +
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Residues in contact with ASN2436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2336B GLN* 3.6 38.2 + - + +
2337B ALA* 5.2 2.8 - - - -
2339B ARG* 3.4 30.3 + - - +
2432B ILE* 2.8 47.6 + - - +
2433B VAL 3.9 3.6 - - - +
2435B ARG* 1.3 77.1 - - - +
2437B HIS* 1.3 59.1 + - - +
2439B ASP* 3.2 3.3 + - - +
2440B ALA* 2.8 31.2 + - - +
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Residues in contact with HIS2437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2231B VAL* 5.0 9.5 - - + +
2343B THR* 5.4 4.5 - - + -
2344B VAL* 2.7 34.0 + - - +
2346B TYR* 3.4 32.0 - + + +
2433B VAL* 3.0 19.0 + - + +
2434B ALA 3.8 2.2 - - - +
2436B ASN* 1.3 76.9 - - - +
2438B ARG* 1.3 63.1 + - - +
2440B ALA* 3.3 12.9 + - + +
2442B ALA* 3.2 36.9 + - + +
2443B PRO 3.0 19.5 + - - -
2444B THR* 2.7 26.2 + - + +
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Residues in contact with ARG2438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2434B ALA 3.1 14.6 + - - +
2435B ARG* 3.2 30.7 + - - +
2437B HIS* 1.3 77.9 - - - +
2439B ASP* 1.3 79.3 + - - +
2441B GLY* 2.8 23.0 + - - -
2442B ALA 3.8 4.5 + - - +
2444B THR* 3.2 12.7 + - - +
2519B GLU* 5.4 2.5 - - - +
2520B TYR* 3.4 18.6 - - + +
2521B ASN* 2.9 44.4 + - + +
2522B GLN* 3.7 24.2 + - - +
2524B GLU* 3.2 27.8 + - - +
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Residues in contact with ASP2439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2339B ARG* 3.4 30.4 + - - +
2435B ARG* 2.8 27.6 + - - +
2436B ASN* 3.2 2.3 + - - +
2438B ARG* 1.3 92.6 + - - +
2440B ALA* 1.3 61.7 + - - +
2441B GLY* 2.9 7.8 + - - -
2522B GLN* 4.0 8.7 + - - +
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Residues in contact with ALA2440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2338B GLU 5.4 0.9 - - - +
2339B ARG* 3.6 36.5 - - + +
2343B THR* 4.4 22.5 - - + +
2436B ASN 2.8 17.3 + - - +
2437B HIS* 3.4 13.0 - - + +
2438B ARG 3.1 0.2 - - - -
2439B ASP* 1.3 77.2 - - - +
2441B GLY* 1.3 59.7 + - - +
2442B ALA* 3.5 0.4 - - + -
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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