Contacts of the helix formed by residues 3374 - 3385 (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 ASP3374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3373C LEU* 1.3 76.4 - - - +
3375C GLN* 1.3 65.0 + - - +
3376C LYS* 3.1 4.2 + - - +
3377C THR* 2.6 42.5 + - - -
3378C ALA* 3.0 20.5 + - - +
3404C LEU* 5.3 0.2 - - - -
3410C THR* 3.9 15.1 - - + +
3413C LYS* 4.7 3.1 - - - +
5461E PRO* 3.8 4.0 - - - +
5462E LYS* 3.2 56.5 + - + +
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Residues in contact with GLN3375 (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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3373C LEU 4.1 0.6 + - - -
3374C ASP* 1.3 73.7 - - - +
3376C LYS* 1.3 62.1 + - - +
3378C ALA* 3.4 8.4 - - - +
3379C MET* 3.0 38.5 + - + +
3400C THR* 4.5 9.4 - - + +
3401C GLU* 3.5 22.2 + - - +
3404C LEU* 3.1 19.2 - - + +
3405C GLY* 2.9 38.7 + - - -
3413C LYS* 3.3 24.8 + - + +
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Residues in contact with LYS3376 (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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3374C ASP* 3.1 11.7 + - - +
3375C GLN* 1.3 75.5 - - - +
3377C THR* 1.3 64.4 + - - +
3379C MET* 3.4 20.6 + - + +
3380C SER* 3.3 23.2 + - - +
5458E ASP* 4.8 14.8 - - + +
5462E LYS* 3.7 27.7 - - - +
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Residues in contact with THR3377 (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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3373C LEU* 3.5 22.9 - - + -
3374C ASP* 2.6 35.4 + - - -
3376C LYS* 1.3 76.0 - - - +
3378C ALA* 1.3 63.5 + - - +
3380C SER* 3.1 4.0 + - - -
3381C LEU* 3.0 24.6 + - + +
5458E ASP 3.6 10.7 + - - +
5459E MET* 3.2 36.1 - - - +
5460E LYS 3.8 4.5 + - - -
5461E PRO* 3.7 14.7 - - + +
5462E LYS* 4.2 1.6 + - - +
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Residues in contact with ALA3378 (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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3373C LEU* 3.8 18.6 - - + +
3374C ASP 3.0 10.9 + - - +
3375C GLN 3.4 10.1 - - - +
3377C THR* 1.3 78.5 - - - +
3379C MET* 1.3 56.8 + - - +
3381C LEU* 3.2 2.7 + - - -
3382C LEU* 2.9 30.8 + - - +
3400C THR* 3.9 6.3 - - + -
3404C LEU* 3.5 32.1 - - + -
3417C PHE* 3.6 12.2 - - + -
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Residues in contact with MET3379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3375C GLN* 3.0 31.8 + - + +
3376C LYS* 3.7 20.0 - - + +
3377C THR 3.3 0.2 - - - -
3378C ALA* 1.3 76.7 - - - +
3380C SER* 1.3 61.3 + - - +
3382C LEU* 3.5 0.6 + - - -
3383C TRP* 3.1 21.8 + - - +
3396C ILE* 3.5 22.6 - - + +
3397C PRO* 4.0 33.2 - - - -
3400C THR* 3.6 22.4 - - + +
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Residues in contact with SER3380 (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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3376C LYS* 3.3 12.1 + - - +
3377C THR 3.1 9.1 + - - -
3379C MET* 1.3 77.7 - - - +
3381C LEU* 1.3 64.7 + - - +
3383C TRP* 3.3 8.2 + - - +
3384C LYS* 3.1 27.6 + - - +
5458E ASP* 3.3 40.1 + - - +
5459E MET* 4.6 5.8 - - - -
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Residues in contact with LEU3381 (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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3306C LEU* 5.3 1.1 - - + +
3308C LEU* 5.6 0.2 - - + -
3366C TYR* 5.2 6.2 - - + -
3367C PRO* 4.0 26.0 - - + +
3368C LEU* 3.8 28.9 - - + -
3373C LEU* 3.9 21.8 - - + -
3377C THR* 3.0 18.7 + - + +
3378C ALA 3.7 3.6 - - - +
3380C SER* 1.3 73.4 - - - +
3382C LEU* 1.3 57.3 + - - +
3384C LYS* 3.2 8.6 + - + +
3385C SER* 2.7 37.8 + - - +
3417C PHE* 3.7 23.6 - - + -
5459E MET* 3.9 33.2 - - + +
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Residues in contact with LEU3382 (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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3378C ALA 2.9 17.6 + - - +
3379C MET 3.7 5.2 - - - +
3380C SER 3.3 0.2 - - - -
3381C LEU* 1.3 76.5 - - - +
3383C TRP* 1.3 62.9 + - - +
3385C SER* 3.3 15.0 + - - -
3386C TYR* 3.6 5.5 + - - -
3389C VAL* 4.1 8.8 - - + +
3391C ILE* 4.0 26.0 - - + +
3396C ILE* 3.6 30.2 - - + +
3399C ALA* 4.2 9.4 - - + -
3400C THR* 3.7 20.2 - - - +
3417C PHE* 4.0 9.8 - - + -
3420C LEU* 4.3 14.6 - - + -
3421C ILE* 3.7 28.5 - - + -
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Residues in contact with TRP3383 (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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3311C ASP* 4.4 1.8 - - - -
3312C PRO* 3.1 50.3 - - + +
3313C ARG* 3.6 42.4 - - + -
3379C MET 3.1 13.2 + - - +
3380C SER* 3.5 11.4 - - - +
3381C LEU 3.2 0.2 - - - -
3382C LEU* 1.3 75.8 - - - +
3384C LYS* 1.3 71.0 + - + +
3386C TYR* 3.0 37.4 + + - +
3391C ILE 4.1 6.1 - - - -
3392C ALA* 4.8 0.2 - - - -
3393C LYS* 3.7 73.0 - - + +
3396C ILE* 4.1 9.8 - - + +
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Residues in contact with LYS3384 (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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3306C LEU* 3.3 20.9 - - + +
3307C ASP 4.4 14.1 - - - +
3308C LEU* 3.3 39.1 + - + +
3310C GLY 3.3 25.9 + - - +
3312C PRO* 3.9 19.2 - - + +
3315C SER* 5.1 0.3 + - - -
3380C SER* 3.1 19.0 + - - +
3381C LEU* 3.2 11.4 + - + +
3383C TRP* 1.3 83.3 - - + +
3385C SER* 1.3 56.7 + - - +
3386C TYR 3.1 3.3 + - - -
3387C PRO* 3.5 8.3 - - - +
5459E MET* 4.1 28.0 - - + -
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Residues in contact with SER3385 (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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3306C LEU* 4.0 5.7 - - - +
3366C TYR* 2.5 38.8 + - - -
3381C LEU 2.7 21.2 + - - -
3382C LEU* 3.6 12.0 - - - -
3383C TRP 3.1 1.0 - - - -
3384C LYS* 1.3 73.6 - - - +
3386C TYR* 1.3 54.7 + - - +
3387C PRO* 3.2 4.0 - - - -
3388C LEU* 2.7 27.4 + - - -
3389C VAL* 3.0 19.0 + - - +
3417C PHE* 4.8 0.5 - - - -
3421C ILE* 4.5 10.6 - - - +
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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