Contacts of the helix formed by residues 4060 - 4064 (chain D) 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 LEU4060 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684D SO4 5.8 0.2 - - - +
4058D PRO* 2.8 30.7 + - + +
4059D PRO* 1.3 76.3 - - - +
4061D GLY* 1.3 68.4 + - - +
4062D PRO* 3.2 3.8 - - - +
4063D LEU* 3.0 17.5 + - - +
4064D ARG* 5.6 0.7 - - - +
4114D GLU* 3.6 40.6 - - + +
4115D ASP* 4.0 15.0 - - + +
685F SO4 3.9 8.8 + - - +
6280F ALA* 3.7 31.4 - - + +
6281F VAL* 4.4 7.4 - - + +
6284F HIS* 3.8 26.5 - - + +
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Residues in contact with GLY4061 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D SO4 5.6 0.6 + - - -
4060D LEU* 1.3 73.0 - - - +
4062D PRO* 1.3 69.2 - - - +
4063D LEU 3.1 1.3 + - - -
4064D ARG* 3.2 25.9 + - - +
4114D GLU* 5.7 0.2 + - - -
4287D ARG* 4.3 17.1 - - - +
6284F HIS* 3.5 23.5 + - - -
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Residues in contact with PRO4062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D SO4 4.8 9.9 + - - +
4060D LEU 3.6 2.5 - - - +
4061D GLY* 1.3 82.6 - - - +
4063D LEU* 1.3 69.9 + - + +
4064D ARG 3.2 1.1 + - - -
4066D THR* 3.4 16.8 - - - +
4287D ARG* 3.7 16.8 + - - -
685F SO4 3.5 20.0 - - - +
6062F PRO* 6.6 0.2 - - + -
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Residues in contact with LEU4063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4057D LYS* 3.9 33.0 - - + +
4058D PRO 3.5 20.4 - - - +
4059D PRO* 3.6 16.4 - - + +
4060D LEU 3.0 15.6 + - - +
4062D PRO* 1.3 83.5 - - + +
4064D ARG* 1.3 64.5 + - - +
4065D PHE 3.4 0.3 + - - -
4066D THR* 2.7 30.3 + - + +
4067D PRO 5.1 0.6 - - - +
4069D GLN* 3.5 35.7 - - + +
4171D ARG* 3.5 10.9 + - - -
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Residues in contact with ARG4064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D SO4 2.9 20.2 + - - -
4059D PRO 3.8 16.1 + - - +
4060D LEU* 6.2 0.8 - - - +
4061D GLY* 3.2 20.5 + - - +
4062D PRO 3.2 1.0 - - - -
4063D LEU* 1.3 80.0 - - - +
4065D PHE* 1.3 99.2 + - + +
4066D THR* 3.4 0.5 + - - +
4114D GLU* 2.7 30.8 + - - -
4171D ARG* 4.6 2.9 - - - +
4175D TRP* 4.1 14.0 - - + +
4286D LEU 2.8 19.8 + - - -
4287D ARG* 2.7 44.2 + - + +
4289D LYS 2.7 25.2 + - - -
4291D GLU 4.1 3.2 - - - +
4294D LEU* 3.3 16.9 - - - +
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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