Contacts of the strand formed by residues 83 - 89 (chain D) in PDB entry 4NY0
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 TYR 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D PHE* 4.2 6.7 - + - -
68D ILE* 3.4 27.5 - - + +
72D VAL* 4.4 7.4 - - + -
77D VAL* 3.6 24.7 - - + +
79D HIS 3.4 23.1 - - - -
80D VAL* 3.2 19.1 + - - +
81D ALA* 4.6 1.6 - - - +
82D CYS* 1.3 82.0 - - + +
84D GLY* 1.3 58.2 + - - +
100D VAL* 4.8 5.0 - - - +
124D LEU* 4.0 19.1 - - + -
125D ARG 3.3 11.0 - - - +
126D ILE* 3.6 25.5 - - + +
128D TYR* 3.6 10.8 - - - -
143D THR* 2.9 34.6 + - + +
146D PHE* 3.9 25.5 - + - +
349D ARG* 5.8 0.2 + - - -
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Residues in contact with GLY 84 (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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68D ILE* 3.9 8.7 - - - -
82D CYS 4.0 0.8 + - - -
83D TYR* 1.3 74.1 - - - +
85D LEU* 1.3 61.0 + - - -
97D TRP* 3.9 11.2 - - - -
98D LEU 5.5 0.9 - - - -
100D VAL* 5.7 2.0 - - - -
124D LEU* 3.5 7.3 - - - +
125D ARG 2.8 32.1 + - - -
127D ARG 4.6 1.2 - - - +
128D TYR* 4.0 19.8 - - - -
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Residues in contact with LEU 85 (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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37D LEU* 5.3 2.7 - - + -
39D VAL* 3.7 28.7 - - + -
64D VAL* 3.6 33.9 - - + +
67D ILE* 4.2 23.6 - - + -
68D ILE* 4.4 4.2 - - + +
84D GLY* 1.3 73.5 - - - -
86D ARG* 1.3 58.3 + - - +
97D TRP* 3.7 7.4 - - - -
98D LEU* 2.9 56.8 + - + +
104D VAL* 6.1 1.1 - - + -
122D TYR* 4.6 12.8 - - + -
123D GLU 3.6 20.0 - - - +
124D LEU* 3.9 8.7 - - + +
128D TYR* 5.2 0.2 + - - -
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Residues in contact with ARG 86 (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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42D TYR* 5.3 0.2 + - - -
85D LEU* 1.3 73.5 - - - +
87D LEU* 1.3 59.8 + - - +
88D SER* 3.6 14.3 + - - +
95D VAL* 3.6 33.4 - - + -
96D HIS 3.8 3.8 - - - +
97D TRP* 3.7 38.9 - - + +
98D LEU* 5.2 0.2 - - - -
121D LYS 3.6 2.8 - - - +
122D TYR* 3.6 1.4 - - - -
123D GLU* 2.9 79.0 + - + +
125D ARG* 3.4 34.4 - - - +
154D ASP* 5.6 0.8 + - - -
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Residues in contact with LEU 87 (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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85D LEU 3.9 1.8 + - - -
86D ARG* 1.3 71.7 - - - +
88D SER* 1.3 58.5 + - - +
89D HIS 4.4 0.3 + - - -
95D VAL* 3.6 2.1 - - - +
96D HIS* 2.8 48.5 + - + +
98D LEU* 4.1 17.0 - - + -
107D VAL* 5.0 0.2 - - + -
111D TYR* 3.5 45.5 - - + -
120D TRP* 3.5 35.4 - - + -
121D LYS 3.5 12.8 - - - +
122D TYR* 3.5 38.1 - - + +
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Residues in contact with SER 88 (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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86D ARG* 3.6 26.2 + - - +
87D LEU* 1.3 75.5 + - - +
89D HIS* 1.3 65.6 + - - +
90D LEU* 3.7 4.0 + - - +
94D GLU 3.8 8.7 - - - -
95D VAL* 4.1 11.3 - - - +
120D TRP* 3.6 6.5 - - - -
121D LYS* 2.8 47.2 + - - +
123D GLU* 4.8 4.8 + - - +
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Residues in contact with HIS 89 (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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88D SER* 1.3 74.2 - - - +
90D LEU* 1.3 61.8 + - - +
91D ARG* 3.5 23.3 - - + +
92D SER* 2.8 47.7 + - - +
94D GLU* 3.2 22.3 + - + +
115D HIS* 3.4 41.2 + + + -
119D GLU* 2.9 47.4 + - + -
120D TRP* 3.5 21.2 - + + -
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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