Contacts of the helix formed by residues 3290 - 3302 (chain C) in PDB entry 2H7C
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 THR3290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C SO4 3.2 18.6 - - - +
3064C ARG* 4.2 0.7 - - - -
3288C GLN 4.9 3.6 - - - +
3289C LYS* 1.3 76.2 - - - +
3291C GLU* 1.3 65.0 + - - +
3292C GLU* 3.6 9.7 + - - +
3293C GLU* 2.7 46.7 + - - +
3294C LEU* 3.0 21.3 + - - +
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Residues in contact with GLU3291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A LYS* 4.5 18.5 + - - +
184C SO4 2.8 17.9 + - - +
3064C ARG* 4.4 0.2 - - - +
3088C THR* 2.6 40.5 + - + +
3112C LEU* 4.1 5.6 - - - +
3113C SER* 3.3 22.4 + - - -
3114C GLU* 3.4 36.0 + - + +
3175C TRP* 3.7 8.0 - - + -
3290C THR* 1.3 70.4 - - - +
3292C GLU* 1.3 59.4 + - - +
3294C LEU* 3.3 1.8 + - - -
3295C LEU* 2.9 27.3 + - + +
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Residues in contact with GLU3292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3290C THR* 3.1 8.7 + - - +
3291C GLU* 1.3 81.4 + - - +
3293C GLU* 1.3 58.9 + - + +
3295C LEU* 3.1 10.3 + - + +
3296C GLU* 2.9 48.8 + - + +
5300E LYS* 3.6 18.5 + - - +
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Residues in contact with GLU3293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3272C ALA* 6.2 0.2 - - - -
3288C GLN 4.4 1.0 - - - +
3289C LYS* 3.1 31.8 + - + +
3290C THR* 2.7 55.3 + - - +
3292C GLU* 1.3 77.9 - - + +
3294C LEU* 1.3 56.9 + - - +
3296C GLU* 3.5 16.4 + - - +
3297C THR* 2.9 29.6 + - - -
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Residues in contact with LEU3294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3064C ARG* 3.4 40.4 - - - +
3065C PHE* 4.5 1.3 - - + -
3174C ILE* 3.8 24.4 - - + +
3175C TRP* 3.4 32.3 - - + +
3272C ALA* 4.8 0.4 - - + -
3286C LEU* 4.0 25.6 - - + +
3289C LYS* 3.8 19.5 - - + -
3290C THR 3.0 13.4 + - - +
3291C GLU 3.8 2.0 - - - +
3293C GLU* 1.3 75.0 - - - +
3295C LEU* 1.3 60.5 + - - +
3297C THR* 3.3 11.0 + - - +
3298C THR* 2.7 31.5 + - - -
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Residues in contact with LEU3295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3088C THR* 4.4 13.5 - - + -
3089C GLN* 3.5 26.5 - - - +
3090C ASP* 4.1 1.3 - - - +
3091C PRO* 4.4 8.5 - - + -
3112C LEU* 4.1 22.4 - - + -
3175C TRP* 3.8 3.5 - - + -
3291C GLU* 2.9 15.6 + - + +
3292C GLU* 3.5 13.5 - - + +
3294C LEU* 1.3 78.5 - - - +
3296C GLU* 1.3 59.1 + - + +
3298C THR* 3.1 9.2 + - - +
3299C LEU* 3.0 55.6 + - + +
5300E LYS* 5.9 6.1 - - - +
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Residues in contact with GLU3296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3292C GLU* 2.9 33.3 + - + +
3293C GLU* 3.7 16.9 - - - +
3295C LEU* 1.3 73.2 - - + +
3297C THR* 1.3 65.6 + - - +
3299C LEU* 3.4 8.6 + - - +
3300C LYS* 3.0 33.4 + - - +
5296E GLU* 2.9 45.7 - - + +
5300E LYS* 3.4 37.6 + - + +
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Residues in contact with THR3297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3174C ILE* 4.1 15.5 - - + -
3268C ILE* 3.9 28.0 - - + +
3271C THR* 3.9 20.7 + - + -
3272C ALA* 3.5 24.4 - - + +
3293C GLU 2.9 15.7 + - - -
3294C LEU* 3.5 13.0 - - + -
3295C LEU 3.2 0.2 - - - -
3296C GLU* 1.3 76.2 - - - +
3298C THR* 1.3 63.7 + - - +
3300C LYS* 3.2 6.0 + - - +
3301C MET* 3.1 31.0 + - + +
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Residues in contact with THR3298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C COA 5.8 2.2 - - - +
3089C GLN* 5.6 2.2 - - - -
3090C ASP* 5.0 11.0 - - + +
3145C MET* 4.3 11.9 - - + -
3173C GLY* 6.3 0.2 - - - -
3174C ILE* 3.5 15.0 + - + +
3175C TRP* 3.9 14.6 - - + -
3294C LEU 2.7 20.6 + - - -
3295C LEU* 3.2 15.9 - - + -
3297C THR* 1.3 77.4 - - - +
3299C LEU* 1.3 70.4 + - + +
3301C MET* 3.2 13.2 + - - +
3302C LYS* 3.4 7.6 + - - -
3303C PHE* 3.8 29.9 + - + -
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Residues in contact with LEU3299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C COA 3.7 34.5 + - - +
3090C ASP* 4.4 16.4 - - + +
3091C PRO* 5.1 5.8 - - + -
3295C LEU* 3.0 39.6 + - + +
3296C GLU* 3.7 13.0 - - - +
3298C THR* 1.3 83.0 - - + +
3300C LYS* 1.3 60.9 + - - +
3302C LYS* 3.2 12.1 + - - +
5E COA 3.4 14.6 + - - -
5299E LEU* 4.8 11.8 - - + +
5300E LYS* 3.9 32.3 - - + +
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Residues in contact with LYS3300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3271C THR* 3.8 35.4 + - + +
3296C GLU* 3.0 25.5 + - - +
3297C THR* 3.2 5.8 + - - +
3299C LEU* 1.3 76.0 - - - +
3301C MET* 1.3 58.3 + - - +
3302C LYS* 3.4 1.2 + - - +
5E COA 4.5 2.6 + - - -
5092E LYS* 3.1 24.8 + - - +
5292E GLU* 3.0 34.0 + - - +
5296E GLU* 3.5 27.6 + - - -
5299E LEU* 4.0 23.6 - - + -
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Residues in contact with MET3301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3174C ILE* 5.7 0.4 - - + -
3264C LEU* 4.0 4.5 - - + -
3267C GLN* 3.5 32.3 - - - +
3268C ILE* 3.8 24.9 - - + -
3271C THR* 3.7 25.4 - - + -
3297C THR* 3.1 27.0 + - + +
3298C THR 3.5 2.2 - - - +
3299C LEU 3.2 0.2 - - - -
3300C LYS* 1.3 74.2 - - - +
3302C LYS* 1.3 79.4 + - - +
3303C PHE* 3.4 51.1 - - + -
3316C GLN* 4.9 4.4 - - + +
5092E LYS* 3.4 5.4 + - - +
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Residues in contact with LYS3302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C COA 2.8 14.8 + - - -
3298C THR 3.4 2.7 + - - -
3299C LEU* 3.2 12.8 + - - +
3300C LYS 3.2 0.2 - - - -
3301C MET* 1.3 87.2 - - - +
3303C PHE* 1.3 61.5 + - - +
3305C SER* 3.7 14.6 + - - +
3307C ASP* 3.0 48.5 + - - +
3309C GLN* 5.5 1.6 - - - +
3316C GLN 5.0 1.6 - - - +
3317C PRO* 5.2 0.7 - - - +
5E COA 2.7 44.7 - - + +
5092E LYS* 2.9 49.3 - - + +
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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