Contacts of the helix formed by residues 92 - 102 (chain D) in PDB entry 4XHW
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 SER 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D LYS 3.6 3.1 + - - -
91D LEU* 1.3 73.4 - - - +
93D PRO* 1.3 76.0 - - - +
94D THR* 3.6 8.6 + - - -
95D GLN* 3.0 45.4 + - - +
96D LEU* 3.1 12.2 + - - +
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Residues in contact with PRO 93 (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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35D ALA* 3.5 34.0 - - + +
38D ARG* 3.7 32.8 - - + +
39D GLU* 3.8 25.1 - - - +
92D SER* 1.3 85.5 - - - +
94D THR* 1.3 57.7 + - - +
96D LEU* 3.2 4.6 + - + +
97D ARG* 2.9 36.6 + - - +
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Residues in contact with THR 94 (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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92D SER* 3.1 7.8 + - - -
93D PRO* 1.3 77.6 - - - +
95D GLN* 1.3 68.1 + - + +
97D ARG* 3.1 9.1 + - + +
98D ARG* 2.9 26.5 + - + +
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Residues in contact with GLN 95 (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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72D LEU 5.6 0.3 - - - +
90D LYS 4.1 3.1 - - - +
91D LEU* 3.5 31.0 - - + +
92D SER* 3.0 43.0 + - - +
94D THR* 1.3 77.7 - - + +
96D LEU* 1.3 57.6 + - - +
98D ARG* 3.4 7.1 + - - +
99D ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 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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31D LEU* 3.5 35.3 - - + +
34D ALA* 3.8 9.4 - - + -
35D ALA* 3.6 25.6 - - + +
38D ARG* 3.7 28.5 - - - +
87D ILE* 3.7 24.9 - - + -
91D LEU* 3.9 21.1 - - + -
92D SER 3.1 12.8 + - - +
93D PRO 3.4 6.7 - - - +
95D GLN* 1.3 77.3 - - - +
97D ARG* 1.3 57.0 + - - +
99D ALA* 3.1 7.0 + - + +
100D ALA* 2.9 29.1 + - - +
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Residues in contact with ARG 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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53A THR* 5.4 6.9 - - - +
32D ILE* 4.1 21.4 + - + +
35D ALA* 3.4 21.3 - - + +
36D ASP* 3.1 23.6 + - - -
39D GLU* 2.2 46.5 + - - +
93D PRO* 2.9 23.4 + - - +
94D THR* 3.1 8.6 + - + +
96D LEU* 1.3 75.7 - - - +
98D ARG* 1.3 57.4 + - - +
100D ALA* 3.9 6.4 - - - +
101D ALA* 2.9 30.3 + - - +
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Residues in contact with ARG 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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72D LEU* 6.3 0.6 - - - +
94D THR* 2.9 19.1 + - + +
95D GLN* 3.7 7.0 - - - +
97D ARG* 1.3 74.8 - - - +
99D ALA* 1.3 67.4 + - - +
101D ALA* 3.7 6.4 - - + +
102D SER* 3.0 35.2 + - - -
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Residues in contact with ALA 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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31D LEU* 4.0 16.2 - - + -
72D LEU* 3.9 33.3 - - + +
95D GLN 3.0 14.9 + - - +
96D LEU* 3.3 11.9 - - + +
98D ARG* 1.3 80.4 - - - +
100D ALA* 1.3 62.7 + - - +
102D SER* 2.5 25.5 + - - -
103D LEU* 3.8 8.7 - - - +
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Residues in contact with ALA 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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28D GLN* 2.9 54.7 + - + +
31D LEU* 3.6 15.8 - - + +
32D ILE* 4.0 15.9 - - + -
96D LEU 2.9 15.2 + - - +
97D ARG 3.9 4.0 - - - +
99D ALA* 1.3 75.9 - - - +
101D ALA* 1.3 61.9 + - - +
102D SER 3.3 0.7 + - - -
103D LEU* 3.3 12.2 + - - +
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Residues in contact with ALA 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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33A ARG* 5.4 4.3 + - - -
28D GLN* 4.7 3.1 + - - +
97D ARG 2.9 20.9 + - - +
98D ARG* 3.8 7.0 - - + +
99D ALA 3.1 0.2 - - - -
100D ALA* 1.3 76.7 - - - +
102D SER* 1.3 57.6 + - - +
103D LEU 3.2 6.0 + - - -
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Residues in contact with SER 102 (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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12D ASN* 2.9 36.1 + - - +
72D LEU* 3.7 14.0 - - - +
98D ARG* 3.0 26.5 + - - -
99D ALA* 2.5 25.1 + - - -
101D ALA* 1.3 76.0 - - - +
103D LEU* 1.3 58.7 + - - +
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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