Contacts of the strand formed by residues 95 - 101 (chain D) in PDB entry 4B3E
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 ALA 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D SER* 3.5 2.4 - - - -
35D ILE* 2.8 39.3 + - + +
38D LEU* 3.8 24.5 - - + -
87D VAL* 4.1 18.4 - - + -
88D THR 3.2 27.6 - - - +
89D ALA* 3.8 0.2 - - - -
93D GLY 3.9 1.2 + - - -
94D VAL* 1.3 70.8 - - - +
96D ASP* 1.3 63.8 + - - +
97D VAL* 3.7 3.3 + - + +
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Residues in contact with ASP 96 (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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33D GLY 3.7 5.7 - - - +
34D SER* 3.2 21.7 + - - -
87D VAL* 5.7 0.5 - - - +
88D THR 4.2 7.0 + - - +
90D ASP* 4.7 4.9 - - - +
94D VAL* 3.7 17.6 + - - +
95D ALA* 1.3 74.9 - - - +
97D VAL* 1.3 61.2 + - - +
98D SER 4.1 0.5 + - - -
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Residues in contact with VAL 97 (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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18D ILE* 4.1 17.0 - - + -
31D VAL* 4.0 13.7 - - + +
32D TRP* 3.2 10.2 - - - +
33D GLY 3.0 34.1 + - - +
35D ILE* 4.4 7.2 - - + -
45D PHE* 4.2 11.7 - - + -
87D VAL* 3.4 31.0 - - + -
95D ALA 4.1 9.0 - - - +
96D ASP* 1.3 75.3 - - - +
98D SER* 1.3 64.7 + - - +
99D ILE* 4.0 25.4 - - + -
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Residues in contact with SER 98 (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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31D VAL 3.4 4.7 - - - -
32D TRP* 4.4 7.3 - - - +
96D ASP 4.1 2.0 + - - -
97D VAL* 1.3 76.3 + - - +
99D ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 99 (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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30D LYS* 3.6 1.0 - - - +
31D VAL* 2.8 47.4 + - + +
45D PHE* 3.8 35.0 - - + -
74D PRO* 6.1 3.8 - - + -
84D LEU* 4.0 22.2 - - + +
86D ASN 5.1 4.9 - - - +
87D VAL* 5.0 4.3 - - + -
97D VAL* 4.0 10.3 - - + -
98D SER* 1.3 81.5 + - - +
100D GLU* 1.3 81.7 + - - +
101D ASP* 4.3 9.6 - - + +
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Residues in contact with GLU 100 (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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23D LYS* 5.2 3.7 + - - -
28D PRO* 4.0 22.9 - - + +
29D VAL 3.4 6.3 - - - +
30D LYS* 3.5 38.5 - - + +
74D PRO* 6.1 0.2 - - - +
75D LYS* 3.2 23.7 + - - -
99D ILE* 1.3 82.2 - - - +
101D ASP* 1.3 61.8 + - - +
102D SER* 5.6 0.2 - - - -
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Residues in contact with ASP 101 (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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28D PRO* 3.5 1.2 - - - +
29D VAL* 2.8 35.5 + - - +
74D PRO* 3.8 15.2 - - - +
75D LYS* 4.8 4.0 + - - +
79D ARG* 2.5 38.2 + - - -
84D LEU* 3.7 15.0 - - + -
99D ILE* 4.2 5.6 - - + +
100D GLU* 1.3 76.3 - - - +
102D SER* 1.3 63.9 + - - +
103D VAL 3.0 5.7 + - - -
104D ILE* 3.0 43.8 + - + +
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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