Contacts of the helix formed by residues 1997 - 2004 (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 ALA1997 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1972D VAL* 4.4 2.9 - - - +
1995E SER* 3.3 10.1 + - - +
1996E GLU* 1.3 78.8 - - - +
1998E THR* 1.3 66.3 + - + +
2002E GLN* 3.4 25.6 - - - +
1998F THR* 5.7 5.4 - - + -
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Residues in contact with THR1998 (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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1972D VAL* 3.4 13.0 - - - -
1973D SER 3.3 20.3 + - - +
1995D SER* 5.1 15.7 - - - +
1997D ALA* 5.6 8.3 - - + -
1995E SER* 3.5 16.9 + - - -
1996E GLU 3.2 0.4 - - - -
1997E ALA* 1.3 83.2 - - + +
1999E SER* 1.3 60.8 + - - +
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Residues in contact with SER1999 (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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1972D VAL* 3.2 19.1 - - - +
1973D SER 3.3 11.2 - - - -
1974D THR* 3.4 11.0 - - - -
1994E PHE* 3.6 17.7 - - - -
1995E SER 3.3 15.2 + - - -
1996E GLU* 2.9 15.1 + - - -
1998E THR* 1.3 78.0 - - - +
2000E SER* 1.3 59.7 + - - +
2001E VAL* 3.0 26.0 + - - +
2002E GLN* 3.4 10.7 + - - +
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Residues in contact with SER2000 (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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1972D VAL* 4.2 2.0 - - - -
1973D SER* 3.6 5.2 + - - -
1974D THR* 2.8 22.3 + - - -
1975D ARG* 3.7 20.9 - - - -
2186D PRO* 4.2 2.0 - - - -
3226D PAL 3.0 26.9 + - - -
1999E SER* 1.3 69.0 - - - +
2001E VAL* 1.3 64.4 + - - +
2002E GLN 3.0 1.3 - - - +
2003E LYS* 3.0 35.4 + - - +
2005E GLU* 3.5 17.0 + - - +
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Residues in contact with VAL2001 (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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1974D THR* 4.3 0.8 + - - -
1970E TYR* 3.6 32.8 - - + +
1994E PHE* 3.9 5.8 - - + -
1996E GLU* 3.6 30.7 - - + +
1999E SER* 3.0 18.1 + - - +
2000E SER* 1.3 76.5 - - - +
2002E GLN* 1.3 65.3 + - - +
2004E GLY* 3.0 14.6 + - - -
2005E GLU* 3.6 21.7 + - - +
2006E SER 6.1 0.2 - - - -
2010E SER* 3.8 13.7 - - - +
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Residues in contact with GLN2002 (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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1972D VAL* 4.0 17.3 - - + -
2149D LYS* 6.0 0.2 + - - -
1996E GLU* 3.5 33.5 + - - +
1997E ALA* 3.4 25.8 + - - +
1999E SER 3.5 14.6 - - - +
2000E SER 3.0 0.2 - - - -
2001E VAL* 1.3 80.3 - - - +
2003E LYS* 1.3 56.7 + - - +
2004E GLY 3.3 3.3 + - - -
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Residues in contact with LYS2003 (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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1971D GLU* 5.9 4.0 - - - -
1972D VAL* 3.7 31.4 - - + +
2024D ARG* 3.5 6.5 - - - +
2085D ARG* 4.2 6.1 - - - +
2146D ARG* 3.7 42.0 + - - +
2150D GLU* 4.2 15.2 + - - +
2186D PRO* 3.7 13.9 - - + +
2188D VAL* 3.9 6.6 - - - +
3226D PAL 2.8 60.0 + - - +
2000E SER* 3.0 22.6 + - - +
2002E GLN* 1.3 75.6 - - - +
2004E GLY* 1.3 55.9 + - - +
2005E GLU 3.6 2.6 + - - -
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Residues in contact with GLY2004 (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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2187D ARG 4.6 6.4 - - - +
2188D VAL* 4.4 19.2 - - - +
2001E VAL 3.0 9.5 + - - -
2002E GLN 3.2 4.2 + - - -
2003E LYS* 1.3 78.1 - - - +
2005E GLU* 1.3 63.3 + - - +
2006E SER* 3.4 3.5 + - - -
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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