Contacts of the strand formed by residues 82 - 87 (chain D) in PDB entry 3SDL
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 LEU 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLU 4.5 3.6 - - - +
81D PRO* 1.3 76.5 - - - +
83D SER* 1.3 62.4 + - - +
84D ILE* 4.2 8.1 - - + -
97D GLU* 3.6 4.0 - - - +
98D VAL* 2.8 65.1 + - + +
99D ARG* 4.2 7.6 - - - -
100D LEU* 4.2 23.1 - - + +
142D LEU* 3.8 14.6 - - + +
143D LYS* 3.8 31.2 - - - +
144D PRO* 3.9 13.9 - - + -
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D LEU* 1.3 76.6 + - - +
84D ILE* 1.3 60.4 + - - +
95D THR* 4.0 13.7 - - - -
96D TYR 3.3 7.1 + - - -
97D GLU* 4.0 16.1 + - - +
144D PRO* 3.5 8.9 - - - +
145D LEU* 2.7 38.3 + - - +
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D LEU* 4.2 12.3 + - + -
83D SER* 1.3 79.7 - - - +
85D LEU* 1.3 65.4 + - - +
86D VAL* 4.7 4.3 - - + -
95D THR* 3.2 8.1 + - - -
96D TYR* 2.8 43.5 + - + +
98D VAL* 4.2 16.2 - - + -
107D LEU* 4.0 33.9 - - + -
142D LEU* 4.2 26.0 - - + -
143D LYS 3.7 17.7 - - - +
145D LEU* 3.9 7.9 - - - +
146D SER* 3.7 9.6 - - - +
148D VAL* 4.4 11.4 - - + -
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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
----------------------------------------------------------
84D ILE* 1.3 76.8 - - - +
86D VAL* 1.3 62.1 + - - +
93D SER* 4.3 21.1 - - - +
94D SER* 3.5 26.7 - - - +
95D THR* 3.9 13.9 - - - +
145D LEU* 4.3 32.5 - - + +
146D SER 3.2 10.1 + - - +
147D THR* 4.4 14.1 - - - +
148D VAL* 2.8 30.8 + - - +
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ILE* 4.7 4.9 - - + -
85D LEU* 1.3 76.8 - - - +
87D ARG* 1.3 64.6 + - - +
88D ASN 3.7 1.5 + - - +
92D ARG 3.6 2.3 - - - +
93D SER* 3.5 1.9 - - - -
94D SER* 3.0 32.1 + - - +
96D TYR* 3.3 31.0 - - + +
107D LEU* 4.5 10.5 - - + -
111D VAL* 3.7 35.7 - - + -
115D GLU* 5.0 3.1 - - - +
124D LEU* 4.2 13.2 - - + -
148D VAL* 3.2 21.3 - - + +
150D MET* 4.3 9.9 - - + -
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Residues in contact with ARG 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 4.2 0.6 - - - -
86D VAL* 1.3 70.3 - - - +
88D ASN* 1.3 75.8 + - - +
91D GLY* 3.6 33.8 + - - +
92D ARG 3.5 3.6 - - - -
93D SER* 3.6 19.6 + - - +
147D THR* 4.5 12.0 + - + +
148D VAL 2.8 14.7 + - - +
149D PHE* 3.6 37.7 - - + +
150D MET* 2.8 30.1 + - - +
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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
------------------------------------------------------------
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