Contacts of the helix formed by residues 3395 - 3405 (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 LEU3395 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3391C ILE* 4.0 11.9 - - + -
3392C ALA* 2.9 30.9 + - + +
3394C GLU* 1.3 85.1 - - + +
3396C ILE* 1.3 67.3 + - - +
3397C PRO* 3.4 2.9 - - - -
3398C GLU* 3.1 28.1 + - - +
3399C ALA* 3.1 21.3 + - - +
3550C LEU* 3.6 35.5 - - + +
3551C PHE* 5.2 7.9 - - + -
3553C LYS* 3.7 31.2 - - + +
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Residues in contact with ILE3396 (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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3379C MET* 3.5 35.2 - - + +
3382C LEU* 3.6 39.0 - - + +
3383C TRP* 4.1 6.3 - - + +
3391C ILE* 3.7 27.1 - - + +
3392C ALA 3.3 6.0 + - - +
3393C LYS* 3.3 25.1 - - + +
3395C LEU* 1.3 76.9 - - - +
3397C PRO* 1.3 63.9 - - + +
3399C ALA* 3.3 2.6 + - - +
3400C THR* 2.7 47.0 + - - +
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Residues in contact with PRO3397 (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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3379C MET* 4.0 26.7 - - - -
3393C LYS 3.6 9.2 - - - +
3394C GLU* 4.1 8.3 - - - +
3395C LEU 3.6 3.8 - - - -
3396C ILE* 1.3 94.5 - - + +
3398C GLU* 1.3 54.1 + - + +
3400C THR* 3.7 0.7 - - - +
3401C GLU* 2.8 37.9 + - - +
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Residues in contact with GLU3398 (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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3394C GLU 3.8 9.7 - - - +
3395C LEU* 3.1 30.8 + - - +
3397C PRO* 1.3 76.9 - - + +
3399C ALA* 1.3 58.4 + - - +
3401C GLU* 3.4 4.3 + - - +
3402C LYS* 2.9 31.1 + - - +
3546C PHE* 4.1 6.5 - - + -
3550C LEU* 3.4 24.6 - - + +
3553C LYS* 3.5 20.4 + - - -
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Residues in contact with ALA3399 (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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3382C LEU* 4.2 13.2 - - + -
3391C ILE* 4.5 4.0 - - + -
3395C LEU 3.1 9.3 + - - +
3396C ILE* 3.7 6.7 - - - +
3398C GLU* 1.3 79.1 - - - +
3400C THR* 1.3 63.3 + - - +
3402C LYS* 3.4 4.7 + - - +
3403C TYR* 3.3 25.3 + - - -
3420C LEU* 3.9 3.3 - - + +
3546C PHE* 4.0 12.3 - - - -
3547C TRP* 3.6 27.8 - - + -
3550C LEU* 3.9 8.9 - - + +
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Residues in contact with THR3400 (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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3375C GLN* 4.0 12.6 - - + +
3378C ALA* 3.9 15.9 - - + -
3379C MET* 3.6 25.5 - - + +
3382C LEU* 3.7 9.4 - - - +
3396C ILE* 2.7 29.0 + - - +
3397C PRO 3.8 2.5 - - - -
3399C ALA* 1.3 73.4 - - - +
3401C GLU* 1.3 60.2 + - - +
3403C TYR* 3.2 1.6 + - - -
3404C LEU* 2.8 54.2 + - + +
3417C PHE* 5.9 1.5 - - + -
3420C LEU* 4.4 8.9 - - + +
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Residues in contact with GLU3401 (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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3375C GLN* 3.5 24.1 + - - +
3397C PRO 2.8 22.7 + - - +
3398C GLU* 3.8 6.1 - - - +
3400C THR* 1.3 73.0 - - - +
3402C LYS* 1.3 60.9 + - - +
3405C GLY* 3.0 42.1 + - - +
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Residues in contact with LYS3402 (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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3398C GLU 2.9 18.4 + - - +
3399C ALA 3.4 7.0 - - - +
3401C GLU* 1.3 80.6 - - - +
3403C TYR* 1.3 68.0 + - + +
3405C GLY 4.9 0.2 + - - -
3406C GLY 5.2 2.3 + - - -
3542C LYS 5.9 0.2 - - - -
3546C PHE* 3.5 53.4 - - + +
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Residues in contact with TYR3403 (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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3399C ALA 3.3 15.9 + - - +
3400C THR 3.2 2.4 + - - +
3402C LYS* 1.3 96.6 - - + +
3404C LEU* 1.3 73.9 + - + +
3406C GLY* 4.6 2.5 + - - -
3416C LEU* 3.0 48.6 - - + +
3419C ASP* 4.1 7.0 - - + -
3420C LEU* 3.5 28.9 - - + -
3423C ASP* 2.6 30.2 + - - +
3543C GLU* 3.6 13.5 - - + +
3546C PHE* 4.4 2.2 - + - -
3547C TRP* 3.0 40.9 + + - -
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Residues in contact with LEU3404 (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* 4.8 1.3 - - + -
3374C ASP 5.1 0.2 - - - +
3375C GLN* 3.1 22.6 - - + +
3378C ALA* 3.5 33.2 - - + -
3400C THR* 2.8 28.2 + - + +
3403C TYR* 1.3 77.6 - - + +
3405C GLY* 1.3 55.8 + - - +
3406C GLY 3.0 11.9 + - - -
3407C THR* 3.1 21.5 + - - +
3413C LYS* 3.1 47.0 - - + +
3416C LEU* 3.4 22.4 - - + +
3417C PHE* 3.5 17.0 - - + +
3420C LEU* 5.5 1.3 - - + -
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Residues in contact with GLY3405 (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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3375C GLN* 2.9 17.2 + - - -
3401C GLU* 3.0 36.9 + - - +
3404C LEU* 1.3 76.1 - - - +
3406C GLY* 1.3 59.9 + - - +
3407C THR* 3.4 2.7 + - - +
3413C LYS* 5.5 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