Contacts of the strand formed by residues 136 - 145 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97J TYR* 3.7 52.3 - - + +
98J LYS* 4.5 5.7 - - - +
129J TYR* 3.7 31.2 - - + -
130J SER 3.7 8.5 - - - +
131J TYR* 3.5 35.6 - - + +
135J GLU* 1.3 77.9 - - - +
137J ILE* 1.3 63.6 + - - +
138J CYS 3.9 8.7 - - - +
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Residues in contact with ILE 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J LEU* 3.6 1.4 - - - -
97J TYR* 2.7 34.9 + - - -
98J LYS* 3.3 23.4 + - + +
99J PRO 5.0 1.1 - - - +
100J LEU* 3.5 31.9 - - + -
101J PRO* 4.6 14.8 - - + -
106J LEU* 3.4 30.7 - - + -
130J SER* 2.9 16.4 + - - +
132J SER* 3.4 17.9 - - - +
135J GLU* 3.4 16.8 - - - +
136J LEU* 1.3 75.9 - - - +
138J CYS* 1.3 58.8 + - + +
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Residues in contact with CYS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J GLY* 4.6 11.7 - - - -
64J ILE* 4.6 7.0 - - - -
94J LEU* 4.0 4.5 - - + -
95J GLU 3.2 12.3 - - - +
96J LEU* 3.8 17.3 - - + -
97J TYR* 4.1 4.7 - - - -
100J LEU* 4.4 8.5 - - - -
106J LEU* 5.7 0.2 - - - -
128J VAL 4.0 0.7 - - - +
129J TYR* 3.6 2.8 - - - -
130J SER* 3.1 48.0 + - - -
136J LEU* 3.9 4.4 - - - +
137J ILE* 1.3 88.0 - - + +
139J HIS* 1.3 60.5 + - - +
140J ASN* 4.3 13.2 - - - -
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Residues in contact with HIS 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J TYR* 3.7 25.4 - + - +
94J LEU* 3.3 5.6 - - - +
95J GLU* 2.9 33.6 + - + +
97J TYR* 3.5 31.2 + - + +
127J ASP* 2.6 33.0 + - + -
128J VAL 3.7 6.3 - - - -
129J TYR* 3.6 34.6 + + + -
138J CYS* 1.3 75.3 - - - +
140J ASN* 1.3 87.5 + - - +
141J GLN* 4.6 2.0 - - + -
162J LYS* 4.3 13.6 - - - -
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Residues in contact with ASN 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J GLY 3.2 20.7 + - - -
62J VAL* 3.6 9.7 - - - -
65J GLY* 3.9 14.1 - - - +
92J GLN* 3.2 18.4 + - - +
93J TYR 3.2 2.9 - - - +
94J LEU* 3.4 23.3 - - - +
127J ASP* 3.2 4.0 - - - -
128J VAL* 2.9 41.4 + - + +
130J SER* 4.9 1.2 + - - -
138J CYS* 4.3 8.7 - - - -
139J HIS* 1.3 77.7 - - - +
141J GLN* 1.3 59.7 - - - +
142J PHE* 3.4 26.7 - - + -
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Residues in contact with GLN 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J GLU 4.7 0.2 - - - -
92J GLN* 3.8 2.6 + - - -
93J TYR* 2.9 44.3 + - + +
125J ILE* 3.8 22.1 - - + +
126J MET 3.4 2.5 - - - +
127J ASP* 2.7 29.3 + - - +
139J HIS* 4.2 4.8 - - - +
140J ASN* 1.3 72.7 - - - +
142J PHE* 1.3 61.8 + - - +
143J SER* 3.6 7.1 + - - -
160J LYS 3.0 25.3 + - - -
161J VAL* 3.6 5.9 - - - +
162J LYS* 2.8 43.9 + - - +
243J LYS* 5.0 4.5 + - - -
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Residues in contact with PHE 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J VAL* 4.1 10.5 - - + -
65J GLY 3.6 23.6 - - - -
66J GLN* 3.9 16.2 - - + -
69J MET* 4.2 18.2 - - + -
89J HIS* 3.6 15.7 - + - +
91J GLU 4.1 0.2 - - - -
92J GLN* 3.0 33.7 - - - -
125J ILE* 3.8 0.5 - - - -
126J MET* 2.9 50.5 + - + +
128J VAL* 3.4 23.6 - - + -
140J ASN* 3.4 25.1 - - + -
141J GLN* 1.3 72.0 - - - +
143J SER* 1.3 61.7 + - - +
144J LEU* 3.5 18.1 + - + +
217J LEU* 5.1 0.4 - - + -
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Residues in contact with SER 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J HIS* 3.9 1.4 - - - -
90J GLY* 2.9 26.7 + - - -
91J GLU* 3.2 49.7 + - - +
123J VAL* 3.9 18.2 - - - +
125J ILE* 4.4 15.9 - - - +
141J GLN* 3.6 5.2 + - - -
142J PHE* 1.3 68.9 - - - +
144J LEU* 1.3 61.4 + - - +
243J LYS* 4.9 2.0 - - - -
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J MET* 4.2 21.5 - - + -
84J PHE* 4.1 25.1 - - + -
87J VAL* 3.1 28.3 - - + -
88J LEU 3.2 8.3 - - - +
89J HIS* 4.2 15.9 - - + -
90J GLY 5.0 0.2 - - - -
123J VAL* 3.3 11.4 - - - +
124J ILE* 3.1 45.5 + - + +
126J MET* 4.5 8.5 - - + -
142J PHE* 3.5 24.5 + - + +
143J SER* 1.3 81.8 + - - +
145J PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J LYS 4.7 0.3 - - - +
87J VAL* 3.6 5.1 - - - +
88J LEU* 2.8 61.1 + - + +
90J GLY* 5.6 2.9 - - - +
118J LYS* 4.4 19.1 - - + -
119J GLY 5.4 5.8 - - - -
122J VAL 3.4 35.2 - - - -
123J VAL* 4.0 9.6 - - + -
124J ILE* 4.8 0.7 - - - -
144J LEU* 1.3 76.5 - - - +
146J LEU* 1.3 77.6 + - - +
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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