Contacts of the strand formed by residues 2050 - 2056 (chain B) in PDB entry 1D1Z
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 TYR2050 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2046B LEU* 3.4 6.4 - - - +
2047B TYR 2.8 32.3 + - - +
2048B HIS* 3.1 27.6 - - + -
2049B GLY* 1.3 83.4 - - - +
2051B ILE* 1.3 63.8 + - - +
2052B TYR* 3.5 21.0 - - + -
3104C LYS* 3.5 45.1 + - + +
4035D GLU* 4.6 11.0 - - + -
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Residues in contact with ILE2051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017B GLU* 3.9 54.7 - - + +
2020B LEU* 4.1 28.0 - - + -
2021B LEU* 4.0 21.1 - - + -
2044B CYS* 4.1 7.0 - - + -
2045B VAL 3.4 2.9 - - - +
2046B LEU* 3.9 18.8 - - + -
2049B GLY 4.7 0.9 - - - +
2050B TYR* 1.3 80.2 - - - +
2052B TYR* 1.3 74.3 + - - +
2053B THR* 4.0 10.3 + - - +
4035D GLU* 5.8 3.1 - - - +
4036D SER* 4.2 4.9 + - - -
5004D SO4 4.9 2.9 + - - -
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Residues in contact with TYR2052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2043B LEU 3.5 1.9 - - - +
2044B CYS* 3.3 4.7 - - - -
2045B VAL* 2.8 37.8 + - + +
2047B TYR* 3.7 31.0 + - + -
2050B TYR* 3.5 32.1 - - + +
2051B ILE* 1.3 73.9 - - - +
2053B THR* 1.3 61.2 + - - +
2054B TYR* 3.7 28.3 - - + +
2095B VAL* 3.7 31.8 - - + +
4035D GLU 3.7 15.7 - - - -
4036D SER* 3.6 26.9 - - - +
4038D PRO* 6.1 2.0 - - + -
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Residues in contact with THR2053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017B GLU* 4.4 4.0 + - - -
2032B ARG* 3.9 14.2 + - - +
2042B CYS* 3.7 33.9 - - + -
2043B LEU 3.5 2.7 - - - -
2044B CYS* 4.2 5.8 - - - +
2051B ILE* 4.0 14.0 + - - +
2052B TYR* 1.3 76.1 + - - +
2054B TYR* 1.3 65.8 + - - +
2055B ARG* 5.3 1.6 - - - +
5002B SO4 4.3 5.2 - - - +
4013D ARG* 4.3 13.1 + - - +
4036D SER* 2.9 16.8 + - - -
4055D ARG* 2.9 41.6 + - - +
5004D SO4 4.8 0.3 + - - -
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Residues in contact with TYR2054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2042B CYS* 3.5 2.1 - - - -
2043B LEU* 2.8 61.9 + - + +
2045B VAL* 4.2 15.0 - - + -
2052B TYR* 3.7 33.8 - - + +
2053B THR* 1.3 77.4 - - - +
2055B ARG* 1.3 66.1 + - - +
2056B VAL 3.4 0.5 + - - -
2066B ALA* 4.9 5.8 - - + -
2067B GLU 3.7 22.2 - - - +
2068B THR* 4.5 1.8 - - - -
2093B GLY 4.4 4.9 - - - -
2094B ILE* 3.6 37.6 - - + -
2095B VAL* 2.9 28.0 + - + +
4036D SER 3.7 20.2 + - - -
4037D VAL* 4.2 11.9 - - + -
4055D ARG* 4.6 1.3 - - - +
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Residues in contact with ARG2055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2034B SER* 4.0 2.4 + - - -
2036B SER* 3.6 10.0 + - - -
2037B VAL* 4.3 14.0 - - - +
2040B VAL* 3.7 25.4 - - + -
2041B TYR 3.4 5.4 - - - -
2042B CYS* 4.0 11.7 - - - +
2053B THR* 4.2 1.0 + - + +
2054B TYR* 1.3 73.7 - - - +
2056B VAL* 1.3 58.5 + - - +
2057B SER* 4.2 3.7 + - - +
2065B SER 3.9 0.5 - - - +
2066B ALA* 3.3 2.6 - - - -
2067B GLU* 2.8 58.2 + - + +
5002B SO4 3.1 31.7 + - - -
4013D ARG* 5.2 1.2 - - - +
4053D THR* 2.8 39.8 + - - +
4054D TYR* 4.5 3.4 - - - +
4055D ARG* 4.3 37.8 - - + +
4067D GLU* 5.3 4.4 + - - +
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Residues in contact with VAL2056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2031B LEU* 4.3 6.7 - - + -
2041B TYR* 2.8 56.2 + - + +
2043B LEU* 3.9 28.7 - - + +
2054B TYR 3.9 0.9 - - - +
2055B ARG* 1.3 75.6 - - - +
2057B SER* 1.3 63.3 + - - +
2065B SER 3.3 9.6 - - - +
2066B ALA* 3.9 17.0 - - + -
2080B ILE* 3.6 34.1 - - + -
2083B LEU* 4.1 14.4 - - + -
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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