Contacts of the strand formed by residues 127 - 134 (chain D) in PDB entry 1H4O
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 ARG 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D GLY 3.4 6.7 - - - +
39D VAL* 4.0 0.6 - - - +
40D PRO* 3.7 11.2 - - + +
46D GLY* 4.2 1.0 - - - -
47D CYS* 3.2 26.5 - - - +
51D HIS* 3.1 53.6 + - + +
125D LEU 3.7 1.4 + - - -
126D LYS* 1.3 71.0 - - - +
128D PHE* 1.3 59.0 + - - +
142D VAL* 3.8 2.9 - - - +
143D GLU* 3.0 33.0 + - + +
146D GLY 2.8 18.9 + - - +
147D THR 3.0 17.0 + - - -
148D GLY 2.9 24.6 + - - -
149D LEU* 3.6 16.6 - - - +
152D SER* 3.1 19.1 - - - +
1162D BEZ 3.2 31.7 + - - -
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.8 27.6 - - + -
37D PHE* 3.2 8.3 - - - +
38D GLY* 2.9 50.0 + - - +
51D HIS* 3.9 2.4 - - - -
73D LEU* 5.1 2.9 - - + -
104D PHE* 3.8 20.9 - + - -
110D LEU* 3.9 22.4 - - + -
125D LEU* 4.2 16.2 - - + -
126D LYS 3.4 18.4 - - - +
127D ARG* 1.3 75.6 - - - +
129D SER* 1.3 71.2 + - - +
130D MET* 3.9 25.6 - - + -
140D LEU* 4.5 1.3 - - + -
141D ASN 3.0 14.4 - - - +
142D VAL* 4.0 14.4 - - + -
152D SER* 3.8 7.4 - - - -
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Residues in contact with SER 129 (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 VAL* 5.1 0.4 - - - -
36D LEU 3.4 7.4 - - - -
37D PHE* 4.0 9.0 - - - -
55D PHE* 4.4 3.1 - - - -
128D PHE* 1.3 74.3 - - - +
130D MET* 1.3 65.3 + - - +
140D LEU* 3.5 2.6 - - - +
141D ASN* 2.7 61.9 + - - +
152D SER* 3.4 23.5 + - - -
157D ILE* 3.5 17.6 - - - +
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Residues in contact with MET 130 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.0 32.1 - - + -
9D ILE* 3.9 24.0 - - - -
35D VAL* 3.3 9.0 - - - +
36D LEU* 2.8 34.6 + - - +
104D PHE* 4.3 6.7 - - + -
110D LEU* 4.2 5.8 - - + -
128D PHE* 3.9 21.8 - - + -
129D SER* 1.3 77.9 - - - +
131D VAL* 1.3 60.9 + - - +
132D VAL* 4.2 9.6 - - + -
137D VAL* 4.0 14.8 - - + -
139D ALA 3.2 10.3 - - - +
140D LEU* 3.6 26.7 - - + -
157D ILE* 3.9 6.5 - - - -
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D LYS* 4.3 15.7 - - + -
34D GLY 3.5 10.1 - - - +
35D VAL* 5.0 0.9 - - + -
130D MET* 1.3 74.4 - - - +
132D VAL* 1.3 64.6 + - - +
133D GLN* 4.8 0.7 - - + +
137D VAL* 3.6 4.7 - - - +
138D LYS* 2.9 38.6 + - + -
139D ALA* 3.0 28.0 + - + +
157D ILE* 3.6 21.7 - - + +
160D GLN* 5.0 9.0 - - + +
161D LEU* 3.7 32.5 - - + -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.1 25.6 - - + -
29D PHE* 3.6 40.6 - - + -
32D LYS 3.8 1.7 - - - +
33D LYS* 3.5 1.6 - - - +
34D GLY 2.8 38.9 + - - +
36D LEU* 4.4 7.2 - - + +
130D MET* 4.2 19.5 - - + +
131D VAL* 1.3 77.4 - - - +
133D GLN* 1.3 63.1 + - - +
135D GLY* 3.6 25.8 - - - +
136D ILE 3.3 5.6 - - - +
137D VAL* 4.9 2.7 - - + -
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Residues in contact with GLN 133 (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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145C ASP* 2.9 36.6 + - + +
148C GLY* 5.0 6.7 - - - -
150C THR* 6.0 3.6 - - - +
32D LYS 3.8 1.3 - - - -
33D LYS* 4.3 21.9 - - + +
131D VAL* 4.2 1.5 - - + -
132D VAL* 1.3 73.9 - - - +
134D ASP* 1.3 77.0 + - + +
136D ILE* 2.8 27.0 + - - +
138D LYS* 3.3 39.5 - - + +
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Residues in contact with ASP 134 (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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144C PRO* 3.9 28.2 - - + +
145C ASP* 4.9 2.9 - - + -
29D PHE 3.4 10.3 + - - -
30D LYS* 3.7 9.4 - - - +
31D GLY* 2.6 32.5 + - - +
32D LYS 2.8 16.6 + - - +
133D GLN* 1.3 75.6 - - + +
135D GLY* 1.3 57.1 + - - +
136D ILE* 3.5 9.2 + - - +
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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