Contacts of the strand formed by residues 1006 - 1010 (chain E) in PDB entry 5DFV
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 SER1006 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004E ALA 4.0 1.8 + - - -
1005E PRO* 1.3 73.6 - - - +
1007E VAL* 1.3 60.1 + - - +
1008E TYR* 3.2 36.7 + - - -
1027E LEU 3.3 4.9 - - - +
1028E VAL* 3.6 0.6 - - - -
1029E LYS* 3.0 34.5 + - - -
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Residues in contact with VAL1007 (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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1005E PRO* 3.9 10.0 + - + +
1006E SER* 1.3 74.4 - - - +
1008E TYR* 1.3 65.4 + - - +
1009E PRO* 4.2 0.3 - - - +
1026E CYS* 3.7 18.4 - - - -
1027E LEU 3.5 4.9 - - - +
1028E VAL* 4.5 2.9 - - + +
1081E CYS* 4.3 0.7 - - - -
1083E VAL* 3.4 49.6 - - + +
1092E VAL* 3.9 31.6 - - + +
1094E LYS* 3.5 36.5 - - + +
2015F GLU* 4.5 1.0 - - - +
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Residues in contact with TYR1008 (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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1006E SER* 3.2 35.6 + - - -
1007E VAL* 1.3 79.4 - - - +
1009E PRO* 1.3 67.3 - - - +
1010E LEU* 5.1 1.6 - - + -
1026E CYS* 3.7 6.5 - - - -
1027E LEU* 2.8 59.7 + - + +
1029E LYS* 4.1 18.5 - - + +
1094E LYS* 4.9 0.9 - - - -
2013F SER* 3.6 12.3 - - - +
2015F GLU* 4.3 11.9 - - + -
2016F GLN* 3.5 56.7 - - + +
2019F SER* 3.8 17.5 + - - -
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Residues in contact with PRO1009 (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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1008E TYR* 1.3 87.0 - - + +
1010E LEU* 1.3 66.8 + - - +
1011E VAL* 4.0 1.3 - - + +
1025E GLY 4.1 4.0 - - - +
1026E CYS* 5.0 4.0 - - - -
1081E CYS* 6.3 0.2 - - + -
1094E LYS* 4.0 18.1 - - + +
1095E LYS 4.6 4.9 - - - +
1096E ILE* 4.0 29.4 - - + +
1097E GLU 5.3 0.7 - - - +
2013F SER* 3.2 37.2 - - - +
2015F GLU* 3.8 26.5 - - + +
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Residues in contact with LEU1010 (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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1008E TYR* 4.2 6.3 - - + +
1009E PRO* 1.3 82.9 - - - +
1011E VAL* 1.3 61.3 + - - +
1024E LEU* 3.8 0.2 - - - +
1025E GLY* 2.9 24.6 + - - +
1026E CYS 3.8 12.8 - - - +
1027E LEU* 3.8 33.7 - - + -
1096E ILE* 3.0 15.4 - - - +
2010F PHE* 3.1 35.6 - - + +
2011F PRO 3.9 22.0 - - - +
2012F PRO* 5.1 1.8 - - + -
2013F SER* 4.7 7.0 - - - +
2016F GLN* 5.7 0.7 - - - +
2023F SER 5.3 1.1 - - - +
2025F VAL* 4.1 28.7 - - + -
2027F PHE* 4.9 2.0 - - + -
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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