Contacts of the strand formed by residues 2080 - 2087 (chain D) in PDB entry 1T77
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 LEU2080 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2078D VAL* 3.5 5.8 - - - +
2079D SER* 1.3 83.4 + - - +
2081D SER* 1.3 94.8 + - - +
2082D THR* 3.7 20.4 - - + -
2097D LEU* 4.8 1.3 - - + +
2098D SER* 3.4 5.9 - - - -
2099D VAL* 3.1 41.0 + - + +
2175D LYS* 3.6 40.2 - - + +
2176D VAL* 4.0 13.5 - - + +
2179D PHE* 3.4 33.0 - - + -
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Residues in contact with SER2081 (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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2078D VAL* 5.3 9.0 - - - -
2080D LEU* 1.3 81.6 - - - +
2082D THR* 1.3 64.5 + - - +
2083D PRO* 4.8 0.3 - - - +
2096D THR* 3.9 12.0 - - - +
2097D LEU 3.4 6.7 - - - -
2098D SER* 4.2 9.6 - - - -
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Residues in contact with THR2082 (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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2080D LEU* 3.7 20.4 - - + -
2081D SER* 1.3 76.6 + - - +
2083D PRO* 1.3 87.7 + - - +
2096D THR* 3.4 7.3 - - - +
2097D LEU* 2.8 38.4 + - + +
2167D PHE* 4.1 16.4 - - + -
2168D PRO* 4.2 2.6 - - - +
2172D THR* 3.5 29.7 + - + +
2175D LYS* 5.8 3.4 - - - -
2176D VAL* 4.3 2.7 - - + -
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Residues in contact with PRO2083 (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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2081D SER 4.8 0.2 - - - +
2082D THR* 1.3 105.3 + - - +
2084D ALA* 1.3 61.2 + - - +
2095D GLY 3.6 9.6 - - - +
2096D THR* 4.4 5.4 - - - +
2167D PHE* 4.1 0.2 - - - -
2168D PRO* 3.4 28.9 - - + +
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Residues in contact with ALA2084 (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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2082D THR 3.6 0.6 + - - +
2083D PRO* 1.3 75.8 - - - +
2085D GLN* 1.3 67.5 + - - +
2094D LYS* 3.6 2.1 - - - +
2095D GLY 2.9 33.4 + - - +
2097D LEU* 4.0 18.4 - - + -
2106D PHE* 3.4 10.8 - - + -
2165D PHE* 4.9 2.9 - - + -
2166D ASN 3.4 13.7 - - - +
2167D PHE* 3.8 22.0 - - + +
2168D PRO* 5.2 0.2 - - - -
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Residues in contact with GLN2085 (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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2084D ALA* 1.3 78.5 - - - +
2086D LEU* 1.3 61.1 + - - +
2087D VAL* 3.6 0.6 + - + -
2092D VAL* 3.5 27.7 - - + +
2093D VAL 3.4 5.8 - - - +
2094D LYS* 4.2 23.4 - - + +
2106D PHE* 4.2 2.2 - - - -
2146D TYR* 4.4 7.1 - - - -
2165D PHE* 3.1 10.9 - - - -
2166D ASN* 2.9 67.3 + - + +
2167D PHE 5.1 3.4 + - - -
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Residues in contact with LEU2086 (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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2085D GLN* 1.3 71.2 - - - +
2087D VAL* 1.3 66.2 + - - +
2088D ALA* 4.7 4.5 - - + +
2091D VAL 3.3 3.2 - - - +
2092D VAL* 3.2 22.9 - - - -
2093D VAL* 2.9 16.6 + - + +
2106D PHE* 3.3 21.6 - - + -
2108D VAL* 4.8 0.2 - - + -
2126D THR* 4.2 14.8 - - + -
2127D GLU 3.9 11.7 - - - +
2128D GLY 3.7 30.5 - - - +
2129D LEU* 3.9 14.4 - - + +
2163D VAL* 3.7 30.5 - - + -
2164D MET 3.7 6.7 - - - +
2165D PHE* 3.9 9.9 - - + -
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Residues in contact with VAL2087 (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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2085D GLN 4.2 8.7 - - - +
2086D LEU* 1.3 76.9 - - - +
2088D ALA* 1.3 60.3 + - - +
2091D VAL 4.0 1.3 - - - -
2092D VAL* 3.9 23.8 - - + -
2146D TYR* 4.1 28.9 - - + -
2163D VAL* 5.6 0.2 - - - +
2164D MET* 2.9 36.7 + - + +
2166D ASN* 4.3 16.2 - - + +
2238D ASN* 3.6 30.5 - - - +
2239D ASP* 4.0 19.3 - - + -
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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