Contacts of the helix formed by residues 2148 - 2152 (chain E) in PDB entry 5G1N
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 GLN2148 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2080E ASP* 2.7 22.7 + - + +
2083E HIS* 3.7 34.3 - - + +
2084E GLY* 4.8 5.7 - - - +
2085E ARG* 5.6 0.3 - - - +
2145E THR* 5.4 1.6 + - - -
2146E ARG* 3.1 41.0 + - - +
2147E ILE* 1.3 66.1 - - - +
2149E LYS* 1.3 64.7 + - - +
2150E GLU* 3.3 10.0 - - - +
2151E ARG* 3.1 21.5 + - + +
2152E PHE* 3.1 15.7 - - - -
3226E PAL 2.7 42.6 + - - +
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Residues in contact with LYS2149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2146E ARG* 4.1 4.0 - - - +
2147E ILE 3.0 8.6 + - - +
2148E GLN* 1.3 69.8 - - - +
2150E GLU* 1.3 69.6 + - - +
2151E ARG 3.1 5.2 + - - -
2152E PHE* 3.2 20.7 + - - +
2158E TYR* 3.1 55.9 - - + +
2002F GLN 5.2 10.0 + - - -
2003F LYS* 5.6 6.7 - - - +
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Residues in contact with GLU2150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2146E ARG* 3.1 39.6 + - - -
2148E GLN* 3.5 4.5 - - - -
2149E LYS* 1.3 83.4 + - - +
2151E ARG* 1.3 82.5 + - + +
2152E PHE 3.7 1.6 - - - +
2002F GLN 5.9 0.7 - - - -
2003F LYS* 3.6 24.1 - - - +
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Residues in contact with ARG2151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1971E GLU* 2.5 35.6 + - - -
2026E PRO* 3.2 33.4 + - - +
2028E PRO* 5.6 0.4 - - - +
2048E GLY* 4.0 12.9 + - - -
2049E VAL* 3.7 24.0 - - + +
2083E HIS* 3.5 29.2 + - + -
2085E ARG* 4.8 1.2 - - - +
2148E GLN* 3.1 23.3 + - + +
2149E LYS 3.1 0.8 - - - -
2150E GLU* 1.3 96.4 + - + +
2152E PHE* 1.3 64.7 + - - +
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Residues in contact with PHE2152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2080E ASP* 3.5 19.7 - - - -
2083E HIS* 4.4 10.8 - + - -
2109E LEU* 3.7 26.9 - - + -
2147E ILE* 3.5 23.1 - - + -
2148E GLN 3.1 37.5 - - - -
2149E LYS* 3.2 16.4 + - - +
2150E GLU 3.7 1.4 - - - +
2151E ARG* 1.3 82.5 - - - +
2153E GLY* 1.3 69.4 + - - +
2154E SER 3.5 14.8 + - - +
2155E THR* 5.5 0.4 - - - -
2157E GLU* 3.7 42.6 - - - -
2158E TYR* 3.8 13.5 - + + -
2161E CYS* 4.1 4.5 - - + -
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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