Contacts of the helix formed by residues 2325 - 2333 (chain A) in PDB entry 5DZZ
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 PHE2325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2275A TYR* 4.7 9.0 - + - -
2278A MET* 3.5 34.5 - - + -
2285A PRO* 3.5 26.7 - - + -
2289A LEU* 3.6 41.1 - - + -
2292A LEU* 3.6 22.4 - - + -
2321A VAL* 4.2 12.6 - - + -
2322A GLY 3.7 2.9 + - - +
2323A ILE 3.2 0.2 - - - -
2324A GLU* 1.3 97.6 - - + +
2326A LYS* 1.3 59.7 + - - +
2327A GLU 3.4 2.5 - - - -
2328A LYS* 3.4 6.9 + - + +
2329A LEU* 2.9 44.2 + - + +
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Residues in contact with LYS2326 (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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2312A VAL* 4.1 5.1 - - + +
2313A GLU* 3.0 30.3 + - - +
2316A TYR* 3.7 49.4 - - + -
2317A LYS* 5.3 0.4 - - - +
2321A VAL* 4.5 6.1 - - + -
2322A GLY 3.5 14.0 + - - +
2323A ILE* 3.6 20.7 + - + +
2325A PHE* 1.3 78.6 - - - +
2327A GLU* 1.3 58.6 + - - +
2329A LEU* 3.3 2.9 + - - +
2330A LEU* 3.0 52.5 + - + +
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Residues in contact with GLU2327 (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 ILE 4.7 2.9 + - - +
2324A GLU 5.4 0.4 - - - +
2325A PHE 3.4 0.4 - - - -
2326A LYS* 1.3 79.0 - - - +
2328A LYS* 1.3 68.1 + - + +
2330A LEU* 3.3 12.4 + - + +
2331A SER* 3.1 22.7 + - - -
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Residues in contact with LYS2328 (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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2289A LEU* 3.8 41.1 - - + +
2293A GLU* 4.6 8.6 - - - +
2324A GLU 4.7 15.2 + - - +
2325A PHE* 3.4 8.4 + - - +
2326A LYS 3.4 0.2 - - - -
2327A GLU* 1.3 83.1 - - + +
2329A LEU* 1.3 59.4 + - - +
2331A SER* 3.6 8.6 + - - -
2332A ALA* 3.2 24.3 + - - +
2363A HIS* 5.1 3.3 + - - +
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Residues in contact with LEU2329 (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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2289A LEU* 3.8 26.2 - - + -
2292A LEU* 3.9 26.7 - - + +
2293A GLU* 4.0 17.9 - - + +
2296A ALA* 3.7 6.2 - - + +
2301A ILE* 4.2 10.1 - - + -
2312A VAL* 3.5 21.3 - - + +
2321A VAL* 3.6 41.3 - - + -
2325A PHE* 2.9 24.3 + - + +
2328A LYS* 1.3 77.1 - - - +
2330A LEU* 1.3 59.7 + - - +
2331A SER 3.2 1.8 - - - -
2332A ALA* 3.3 3.8 + - - +
2333A GLU* 3.0 27.9 + - - +
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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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2312A VAL* 3.7 24.2 - - + -
2313A GLU* 4.3 21.3 - - + +
2326A LYS* 3.0 48.3 + - + +
2327A GLU* 3.3 9.6 + - - +
2329A LEU* 1.3 75.8 - - - +
2331A SER* 1.3 61.4 + - - +
2333A GLU* 3.3 24.0 + - - +
2334A ARG* 3.6 12.1 + - - +
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Residues in contact with SER2331 (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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2327A GLU* 3.1 13.9 + - - -
2328A LYS* 3.6 12.3 - - - -
2329A LEU 3.2 0.2 - - - -
2330A LEU* 1.3 77.1 - - - +
2332A ALA* 1.3 61.6 + - - +
2334A ARG* 3.0 52.8 + - - +
2339A TYR* 3.5 8.7 + - - -
2359A ILE* 5.0 2.8 - - - +
2363A HIS* 5.0 9.6 - - - -
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Residues in contact with ALA2332 (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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2293A GLU* 3.6 42.0 - - + +
2296A ALA* 4.1 3.1 - - + -
2297A ALA* 3.5 8.8 - - - +
2328A LYS 3.2 10.4 + - - +
2329A LEU 3.3 5.6 + - - +
2331A SER* 1.3 75.0 - - - +
2333A GLU* 1.3 56.4 + - - +
2334A ARG 3.1 5.4 - - - -
2335A ALA* 3.2 25.8 + - - +
2339A TYR* 4.5 5.4 - - - -
2363A HIS* 4.6 4.9 - - + -
2367A LEU* 4.5 13.0 - - + -
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Residues in contact with GLU2333 (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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2214A ARG* 2.5 34.6 + - - +
2296A ALA 3.5 17.0 - - - +
2299A GLY 4.3 1.0 - - - +
2311A PRO* 3.4 5.6 - - - +
2312A VAL* 3.2 41.5 + - + +
2313A GLU 4.8 0.9 + - - -
2329A LEU 3.0 16.3 + - - +
2330A LEU* 3.6 18.1 - - - +
2331A SER 3.2 0.6 - - - -
2332A ALA* 1.3 73.4 - - - +
2334A ARG* 1.3 60.4 + - - +
2335A ALA 3.0 5.6 - - - -
2336A VAL* 3.2 20.9 - - + +
2337A THR* 3.3 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