Contacts of the strand formed by residues 151 - 157 (chain D) in PDB entry 4HXD
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 HIS 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C 4LJ 3.5 12.8 - - + +
34D GLN 3.1 20.5 + - - -
35D PRO 4.1 6.7 - - - -
36D GLY* 4.2 5.7 - - - -
40D CYS* 3.9 18.4 - - + -
146D HIS* 3.3 12.0 + - - -
147D VAL* 2.8 47.1 + - + +
150D THR* 1.3 82.2 - - + +
152D PHE* 1.3 74.3 + - - +
153D ASP* 2.7 42.3 + - - -
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Residues in contact with PHE 152 (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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73C LEU* 4.9 3.1 - - + -
74C ARG 3.9 0.9 - - - -
75C GLY* 3.5 41.3 - - - -
34D GLN* 3.4 5.0 - - - +
40D CYS* 3.4 13.1 - - - +
41D PHE* 3.8 24.0 - + + +
44D SER* 2.8 23.8 + - - +
100D GLY 3.8 7.2 - - - -
101D GLY* 4.1 14.6 - - - -
118D LEU* 3.7 28.5 - - + -
144D LEU* 4.1 16.8 - - + -
145D MET 3.1 14.8 - - - -
146D HIS* 3.1 37.2 - + + -
151D HIS* 1.3 90.3 + - - +
153D ASP* 1.3 57.9 + - - +
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Residues in contact with ASP 153 (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* 4.4 3.6 - - + -
32D ILE 4.0 4.3 - - - +
33D ARG* 2.8 38.0 + - - -
34D GLN* 2.8 24.1 + - - +
44D SER* 3.5 7.7 + - - -
144D LEU* 3.6 6.8 - - - +
145D MET* 2.9 51.2 + - + +
147D VAL* 4.9 3.3 - - - +
151D HIS* 2.7 34.2 + - - -
152D PHE* 1.3 73.6 - - - +
154D ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 154 (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* 3.6 5.4 - - - +
32D ILE* 2.9 43.7 + - + +
34D GLN* 4.0 14.6 - - - +
44D SER* 3.9 22.8 + - - +
47D GLU* 4.2 7.2 - - + -
48D LEU* 4.1 16.8 - - + -
143D ASN 4.1 3.1 - - - -
153D ASP* 1.3 75.7 - - - +
155D LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 155 (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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25D VAL* 4.1 7.0 - - + -
29D PHE* 3.7 42.2 - - + -
30D GLU 3.4 3.4 - - - +
31D VAL* 3.8 26.0 - - + -
48D LEU* 3.4 15.6 - - - +
119D TRP* 4.0 27.1 - - + +
143D ASN* 3.0 32.8 + - + +
144D LEU 4.2 0.9 - - - +
145D MET* 3.9 34.1 - - + +
154D ALA* 1.3 81.2 - - - +
156D ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 156 (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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29D PHE* 3.2 8.6 - - - -
30D GLU* 2.7 56.2 + - - +
32D ILE* 3.7 24.0 - - + +
47D GLU* 2.9 41.8 + - - -
48D LEU* 3.9 17.2 + - + +
50D PHE 5.4 1.6 + - - -
143D ASN* 5.5 0.4 - - - +
155D LEU* 1.3 77.7 - - - +
157D ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 157 (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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4D LEU* 5.0 17.3 - - + -
28D TYR 3.6 9.2 - - - +
29D PHE* 3.6 16.2 - - + -
30D GLU* 5.5 0.7 - - - -
138D VAL* 3.8 6.5 - - + +
139D SER* 3.6 31.0 - - - +
141D ALA 5.4 0.4 - - - +
143D ASN* 3.2 31.2 - - - +
156D ARG* 1.3 76.7 - - - +
158D ILE* 1.3 76.2 + - - +
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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