Contacts of the strand formed by residues 136 - 145 (chain D) in PDB entry 1S9C
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 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D TYR* 3.7 53.2 - - + +
98D LYS* 4.4 6.6 - - - +
129D TYR* 3.8 30.1 - - + -
130D SER 3.6 9.6 - - - +
131D TYR* 3.4 33.7 - - + +
134D LYS 4.0 1.2 + - - -
135D GLU* 1.3 75.5 - - - +
137D ILE* 1.3 64.6 + - - +
138D CYS 3.8 8.3 - - - +
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Residues in contact with ILE 137 (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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96D LEU* 3.7 1.6 - - - -
97D TYR* 2.9 28.0 + - - -
98D LYS* 3.4 22.8 + - + +
99D PRO 4.9 0.9 - - - +
100D LEU* 3.4 33.4 - - + -
101D PRO* 4.5 16.4 - - + -
106D LEU* 3.3 30.5 - - + -
130D SER 2.7 16.6 + - - +
132D SER* 3.5 18.8 - - - +
135D GLU* 3.8 15.9 - - - +
136D LEU* 1.3 78.0 - - - +
138D CYS* 1.3 61.7 + - + +
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Residues in contact with CYS 138 (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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61D GLY* 4.5 7.2 - - - -
64D ILE* 4.5 9.9 - - - -
94D LEU* 4.1 4.9 - - + -
95D GLU 3.3 11.0 - - - +
96D LEU* 3.8 18.8 - - + -
97D TYR* 4.2 4.3 - - - -
100D LEU* 4.5 10.8 - - - -
128D VAL 4.0 0.2 - - - +
129D TYR* 3.6 2.6 - - - -
130D SER* 3.0 53.1 + - - +
136D LEU* 3.8 3.7 - - - +
137D ILE* 1.3 84.9 - - + +
139D HIS* 1.3 61.1 + - - +
140D ASN* 4.3 13.5 - - - -
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Residues in contact with HIS 139 (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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93D TYR* 3.7 26.1 - + - +
94D LEU* 3.3 6.8 - - - +
95D GLU* 2.9 33.8 + - + +
97D TYR* 3.6 29.8 + - + -
127D ASP* 2.7 30.0 + - - -
128D VAL 3.7 6.5 - - - -
129D TYR* 3.6 33.5 + + + -
138D CYS* 1.3 75.6 - - - +
140D ASN* 1.3 89.6 + - - +
141D GLN* 4.5 3.4 - - + -
162D LYS* 4.3 14.7 - - + -
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Residues in contact with ASN 140 (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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61D GLY 3.1 20.5 + - - -
62D VAL* 3.6 11.4 - - - -
65D GLY* 3.9 14.8 - - - +
92D GLN* 3.3 16.7 + - - +
93D TYR 3.3 2.0 - - - -
94D LEU* 3.4 21.6 - - - +
127D ASP* 3.3 2.1 - - - -
128D VAL* 2.9 40.7 + - + +
130D SER* 4.7 0.4 + - - -
138D CYS* 4.3 8.7 - - - -
139D HIS* 1.3 81.2 - - - +
141D GLN* 1.3 60.9 + - - +
142D PHE* 3.4 26.9 - - + -
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Residues in contact with GLN 141 (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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91D GLU 4.6 0.3 - - - -
92D GLN* 3.8 4.4 - - - -
93D TYR* 2.8 44.1 + - + +
125D ILE* 3.7 22.2 - - + +
126D MET 3.5 2.0 - - - +
127D ASP* 2.9 28.3 + - - +
139D HIS* 4.2 5.8 + - - +
140D ASN* 1.3 72.8 - - - +
142D PHE* 1.3 59.4 + - - +
143D SER* 3.6 6.4 + - - -
160D LYS 2.6 29.5 + - - -
161D VAL* 3.7 7.6 - - - +
162D LYS* 2.9 39.7 + - - +
243D LYS* 4.9 4.3 + - - -
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Residues in contact with PHE 142 (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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62D VAL* 4.1 10.8 - - + -
65D GLY 3.7 17.7 - - - -
66D GLN* 3.8 21.1 - - + -
69D MET* 3.5 24.9 - - + -
89D HIS* 3.6 13.5 - + - +
91D GLU 4.2 0.4 - - - -
92D GLN* 3.2 28.0 - - - -
124D ILE 3.7 0.3 - - - +
125D ILE* 3.7 1.6 - - - +
126D MET* 3.0 50.6 + - + +
128D VAL* 3.3 33.9 - - + -
140D ASN* 3.4 16.2 - - + -
141D GLN* 1.3 71.6 - - - +
143D SER* 1.3 60.7 + - - +
144D LEU* 3.6 16.8 + - + +
217D LEU* 4.9 1.1 - - + -
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Residues in contact with SER 143 (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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89D HIS* 3.7 2.8 - - - -
90D GLY* 2.9 27.0 + - - -
91D GLU* 3.2 48.2 + - - +
123D VAL* 4.1 15.9 - - - +
124D ILE 4.0 2.9 - - - -
125D ILE* 4.4 12.3 - - - +
141D GLN* 3.6 6.3 + - - -
142D PHE* 1.3 69.6 - - - +
144D LEU* 1.3 61.4 + - - +
145D PHE* 5.9 0.5 - - - +
161D VAL* 6.4 0.7 - - - -
243D LYS* 5.0 2.0 - - - -
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Residues in contact with LEU 144 (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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69D MET* 4.1 26.0 - - + -
84D PHE* 5.2 9.9 - - + -
87D VAL* 3.7 18.4 - - + -
88D LEU 3.4 8.7 - - - +
89D HIS* 4.5 8.7 - - + -
123D VAL* 3.4 8.7 - - - +
124D ILE* 2.8 59.4 + - + +
126D MET* 4.5 22.0 - - + -
142D PHE* 4.0 21.5 - - + +
143D SER* 1.3 81.2 + - - +
145D PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 145 (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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86D LYS 4.4 0.5 - - - +
87D VAL* 3.4 4.6 - - - +
88D LEU* 2.8 60.2 + - + +
90D GLY* 5.3 6.3 - - - +
122D VAL 3.3 31.4 - - - -
123D VAL* 4.1 13.9 - - + -
124D ILE* 4.6 0.7 - - - +
143D SER* 5.3 1.8 - - - +
144D LEU* 1.3 77.2 - - - +
146D LEU* 1.3 78.4 + - - +
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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