Contacts of the strand formed by residues 78 - 83 (chain L) in PDB entry 1DH6
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 PHE 78 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45L GLN* 4.4 11.7 - - - -
55L LEU* 3.8 25.4 - - + -
56L ILE* 3.6 15.9 - - + +
70L ARG* 2.8 19.2 + - - -
74L VAL* 3.9 22.9 - - + -
75L PRO* 3.0 30.4 + - + +
77L ARG* 1.4 88.5 - - - +
79L SER* 1.4 56.3 + - - +
91L LEU* 4.5 5.2 - - + -
92L THR 3.9 2.9 - - - -
93L ILE* 3.8 24.7 - - + +
100L ASP* 3.3 30.3 - - - -
104L TYR* 3.4 33.4 - + - -
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Residues in contact with SER 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ILE* 4.4 0.7 - - - -
70L ARG* 2.8 25.9 + - - +
76L ASP 2.9 14.0 + - - -
77L ARG 3.5 1.7 + - - -
78L PHE* 1.4 69.6 - - - +
80L GLY* 1.4 61.6 + - - +
91L LEU* 4.2 3.7 - - - +
92L THR* 2.9 45.2 + - - +
94L SER* 5.9 2.5 - - - -
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Residues in contact with GLY 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L TRP* 5.2 0.4 - - - -
56L ILE* 4.0 16.8 - - - +
67L ALA 3.6 16.2 - - - -
68L SER* 3.4 16.7 + - - +
79L SER* 1.4 75.1 - - - +
81L SER* 1.4 70.0 + - - -
90L THR* 3.5 12.1 - - - -
91L LEU* 4.3 8.7 - - - -
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Residues in contact with SER 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ALA* 3.5 9.7 + - - +
68L SER* 4.6 6.6 - - - -
80L GLY* 1.4 79.1 + - - -
82L GLY* 1.4 57.4 + - - +
89L PHE* 3.5 10.2 - - - +
90L THR* 2.8 46.9 + - - +
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Residues in contact with GLY 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ASN* 3.9 1.9 + - - -
67L ALA* 3.8 14.6 - - - +
81L SER* 1.4 76.5 - - - +
83L SER* 1.4 66.6 + - - -
88L ASP 3.7 9.9 - - - -
89L PHE* 3.6 9.0 - - - -
90L THR* 6.3 0.4 - - - -
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Residues in contact with SER 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU* 5.5 6.9 - - - +
39L ASN* 3.7 14.4 - - - -
82L GLY* 1.4 75.5 - - - -
84L GLY* 1.4 61.1 + - - +
87L THR* 3.1 9.2 + - - -
88L ASP 3.0 16.4 + - - +
89L PHE* 3.5 12.0 - - - -
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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