Contacts of the strand formed by residues 136 - 145 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.6 56.3 - - + +
98A LYS* 4.5 5.4 - - - +
129A TYR* 3.9 23.8 - - + -
130A SER 3.5 16.6 - - - +
131A TYR* 3.6 28.3 - - + -
134A LYS 3.8 2.8 + - - -
135A GLU* 1.3 78.1 - - - +
137A ILE* 1.3 60.1 + - - +
138A CYS 3.7 15.5 - - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.6 1.0 - - - -
97A TYR* 2.7 34.7 + - - +
98A LYS* 3.3 23.1 + - + +
99A PRO 5.1 1.1 - - - +
100A LEU* 3.6 31.2 - - + -
101A PRO* 4.7 13.9 - - + -
106A LEU* 3.5 17.3 - - + -
130A SER 2.8 16.5 + - - +
132A SER* 3.2 35.9 - - - +
135A GLU* 4.2 12.8 - - + +
136A LEU* 1.3 78.5 - - - +
138A CYS* 1.3 58.1 + - + +
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 4.4 15.7 - - - -
64A ILE* 4.5 6.1 - - - -
94A LEU* 4.1 4.0 - - + -
95A GLU 3.2 11.7 - - - +
96A LEU* 3.8 18.6 - - + -
97A TYR* 4.1 3.1 - - - -
100A LEU* 4.5 9.0 - - - -
106A LEU* 5.8 0.2 - - - -
128A VAL 4.1 0.5 - - - +
129A TYR* 3.7 2.3 - - - -
130A SER* 3.0 49.7 + - - -
136A LEU* 3.7 4.4 - - - +
137A ILE* 1.3 84.0 - - + +
139A HIS* 1.3 61.2 + - - +
140A ASN* 4.3 13.7 - - - -
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.6 23.9 - + - +
94A LEU* 3.3 5.4 - - - +
95A GLU* 2.9 34.8 + - + +
97A TYR* 3.6 27.2 + - + -
127A ASP* 2.7 32.1 + - - -
128A VAL 3.7 7.2 - - - -
129A TYR* 3.6 37.3 + + + -
138A CYS* 1.3 75.3 - - - +
140A ASN* 1.3 89.1 + - - +
141A GLN* 4.7 2.5 - - + -
162A LYS* 4.4 14.0 - - - -
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY 3.0 21.7 + - - -
62A VAL* 3.5 12.2 - - - -
65A GLY* 4.0 13.3 - - - +
92A GLN* 3.2 17.7 + - - +
93A TYR 3.2 3.8 - - - +
94A LEU* 3.4 22.1 - - - +
127A ASP* 3.3 0.9 - - - -
128A VAL* 2.9 42.2 + - + +
130A SER* 4.8 0.6 + - - -
138A CYS* 4.3 8.7 - - - -
139A HIS* 1.3 80.0 - - - +
141A GLN* 1.3 61.1 + - - +
142A PHE* 3.4 25.4 - - + -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU 4.6 0.2 - - - -
92A GLN* 3.7 3.8 + - - +
93A TYR* 2.8 43.8 + - + +
125A ILE* 3.6 22.4 - - + +
126A MET 3.7 1.3 - - - -
127A ASP* 2.8 31.3 + - - +
139A HIS* 4.3 4.7 - - - +
140A ASN* 1.3 73.6 - - - +
142A PHE* 1.3 61.2 + - - +
143A SER* 3.6 5.7 + - - -
160A LYS 3.1 25.5 + - - -
161A VAL* 3.5 11.5 - - - +
162A LYS* 3.0 40.0 + - - +
243A LYS* 4.8 4.9 + - - -
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Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.0 11.7 - - + -
65A GLY 3.7 18.8 - - - -
66A GLN* 3.8 20.4 - - + -
69A MET* 3.5 26.7 - - - -
89A HIS* 3.9 13.2 - + - +
91A GLU 4.1 0.2 - - - -
92A GLN* 3.2 29.8 - - - +
124A ILE 3.8 0.7 - - - +
125A ILE* 3.7 1.7 - - - +
126A MET* 3.0 46.2 + - + +
128A VAL* 3.4 23.1 - - + -
140A ASN* 3.4 24.7 - - + -
141A GLN* 1.3 72.7 - - - +
143A SER* 1.3 60.3 + - - +
144A LEU* 3.7 16.5 + - + +
217A LEU* 4.8 1.1 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS* 3.7 3.3 - - - -
90A GLY* 2.8 32.7 + - - -
91A GLU* 3.2 49.5 + - - +
123A VAL* 4.2 15.9 - - - +
124A ILE 4.0 3.8 - - - -
125A ILE* 4.5 12.7 - - - +
141A GLN* 3.6 5.9 + - - -
142A PHE* 1.3 71.0 - - - +
144A LEU* 1.3 54.9 + - - +
145A PHE* 6.1 0.9 - - - -
161A VAL* 6.1 0.7 - - - -
243A LYS* 5.2 1.3 - - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A MET* 4.3 29.6 - - + -
87A VAL* 3.9 18.2 - - + -
88A LEU 3.2 2.2 - - - +
89A HIS* 4.3 17.9 - - + -
123A VAL* 3.5 6.4 - - - +
124A ILE* 2.9 59.1 + - + +
126A MET* 5.0 12.6 - - + -
142A PHE* 4.2 20.4 - - + +
143A SER* 1.3 78.7 - - - +
145A PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.0 12.5 - - - +
88A LEU* 2.4 71.6 + - + +
90A GLY* 4.7 11.2 - - - +
122A VAL 4.1 3.1 - - - -
123A VAL* 3.7 23.8 - - + -
124A ILE* 6.0 0.4 - - - -
143A SER* 4.0 1.5 + - - -
144A LEU 1.3 69.6 - - - -
146A LEU* 1.3 92.8 + - - +
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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