Contacts of the strand formed by residues 136 - 146 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G TYR* 3.6 52.6 - - + +
98G LYS* 4.6 4.5 - - - +
129G TYR* 3.8 26.2 - - + -
130G SER 3.4 16.8 - - - +
131G TYR* 3.5 30.7 - - + +
135G GLU* 1.3 83.5 + - - +
137G ILE* 1.3 59.8 + - - +
138G CYS 3.8 13.9 - - - +
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Residues in contact with ILE 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G LEU* 3.5 1.0 - - - -
97G TYR* 2.6 33.9 + - - -
98G LYS* 3.3 27.9 + - + +
99G PRO 4.8 2.7 - - - +
100G LEU* 3.5 30.5 - - + -
101G PRO* 4.5 16.2 - - + -
106G LEU* 3.7 28.7 - - + -
130G SER* 2.9 16.0 + - - +
132G SER* 4.0 22.7 - - - +
135G GLU* 4.8 3.4 - - + -
136G LEU* 1.3 77.5 - - - +
138G CYS* 1.3 56.1 + - + +
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Residues in contact with CYS 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G GLY* 4.3 15.9 - - - -
64G ILE* 4.6 5.2 - - - -
94G LEU* 3.9 3.1 - - + -
95G GLU 3.1 12.8 - - - +
96G LEU* 3.6 19.1 - - + -
97G TYR* 4.0 4.3 - - - -
100G LEU* 4.4 9.2 - - - -
106G LEU* 5.9 0.2 - - - -
128G VAL 4.2 0.5 - - - +
129G TYR* 3.8 0.3 - - - -
130G SER* 3.1 47.2 + - - -
136G LEU* 3.8 5.5 - - - +
137G ILE* 1.3 84.1 - - + +
139G HIS* 1.3 62.2 + - - +
140G ASN* 4.2 14.8 - - - -
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Residues in contact with HIS 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G TYR* 3.6 25.5 - + - +
94G LEU* 3.2 4.6 - - - -
95G GLU* 2.8 35.8 + - + +
97G TYR* 3.6 27.7 + - + +
127G ASP* 2.7 31.9 + - - -
128G VAL 3.7 7.6 - - - -
129G TYR* 3.6 36.0 + + + -
138G CYS* 1.3 75.2 - - - +
140G ASN* 1.3 88.2 + - - +
141G GLN* 4.6 2.9 - - + -
162G LYS* 4.7 13.7 - - + -
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Residues in contact with ASN 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLY 2.9 22.9 + - - -
62G VAL* 3.3 12.0 - - - -
65G GLY* 3.9 14.1 - - - +
92G GLN* 3.1 19.2 + - - +
93G TYR 3.1 4.0 - - - +
94G LEU* 3.3 23.9 - - - +
127G ASP* 3.4 1.0 - - - -
128G VAL* 3.0 40.8 + - + +
130G SER* 4.9 0.4 + - - -
138G CYS* 4.2 7.7 - - - -
139G HIS* 1.3 80.4 - - - +
141G GLN* 1.3 60.6 + - - +
142G PHE* 3.4 25.6 - - + -
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Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLU 4.6 0.3 - - - -
92G GLN* 3.7 3.9 + - - -
93G TYR* 2.7 44.2 + - + +
125G ILE* 3.4 24.0 - - + +
126G MET 3.6 3.4 - - - +
127G ASP* 2.7 28.1 + - - +
139G HIS* 4.2 4.6 - - - +
140G ASN* 1.3 73.1 - - - +
142G PHE* 1.3 60.5 + - - +
143G SER* 3.6 5.5 + - - -
160G LYS 2.6 29.7 + - - -
161G VAL* 3.3 25.5 - - - +
162G LYS* 3.4 22.7 + - - +
243G LYS* 4.7 5.5 + - - -
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Residues in contact with PHE 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G VAL* 3.6 17.5 - - + -
65G GLY 3.5 6.5 - - - -
66G GLN* 3.5 28.7 - - + -
69G MET* 3.5 41.1 - - + -
89G HIS* 4.1 2.5 - + - +
91G GLU 4.0 0.4 - - - -
92G GLN* 2.9 30.7 - - - -
124G ILE 3.7 3.1 - - - +
125G ILE* 3.7 0.3 - - - -
126G MET* 3.0 38.5 + - + +
128G VAL* 3.5 23.1 - - + -
140G ASN* 3.4 23.1 - - + -
141G GLN* 1.3 71.6 - - - +
143G SER* 1.3 61.4 + - - +
144G LEU* 3.7 15.9 + - + +
217G LEU* 4.4 2.2 - - + -
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Residues in contact with SER 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G HIS* 3.6 2.3 - - - -
90G GLY* 2.7 33.4 + - - -
91G GLU* 3.0 49.1 + - - +
123G VAL* 3.8 18.5 - - - +
124G ILE 4.3 2.2 - - - -
125G ILE* 4.5 14.1 - - - +
141G GLN* 3.6 5.7 + - - -
142G PHE* 1.3 72.0 - - - +
144G LEU* 1.3 53.2 + - - +
161G VAL* 5.9 0.9 - - - -
243G LYS* 5.5 1.3 - - - -
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G MET* 4.0 35.2 - - + +
74G LEU* 4.4 24.2 - - + -
87G VAL* 4.3 18.8 - - + -
88G LEU 3.4 10.5 - - - +
89G HIS* 4.3 12.8 - - + -
90G GLY* 4.6 0.9 - - - -
123G VAL* 3.3 12.9 - - - +
124G ILE* 3.1 50.9 + - + +
126G MET* 5.1 9.4 - - + -
142G PHE* 4.1 12.8 - - + +
143G SER* 1.3 80.3 - - - +
145G PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G VAL* 3.4 4.9 - - - -
88G LEU* 2.6 55.8 + - + +
90G GLY* 4.5 7.8 - - - +
118G LYS* 4.2 15.7 - - + -
120G SER* 4.4 9.6 - - - -
121G GLY* 3.7 34.5 - - - -
122G VAL 3.5 2.5 - - - -
123G VAL* 3.7 28.9 - - + -
144G LEU* 1.3 75.1 - - - +
146G LEU* 1.3 62.5 + - - +
147G VAL* 3.8 26.1 + - + -
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Residues in contact with LEU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PHE* 4.1 11.7 - - + -
74G LEU* 4.6 5.8 - - + -
82G ILE* 3.8 36.6 - - + -
83G ASN 5.7 0.4 - - - +
86G LYS* 3.7 4.9 - - + +
87G VAL* 3.4 40.4 - - + -
121G GLY* 2.8 25.0 - - - -
122G VAL* 2.8 35.6 + - + +
124G ILE* 4.7 10.5 - - + -
145G PHE* 1.3 72.2 - - - +
147G VAL* 1.3 65.3 + - - +
149G SER* 3.1 18.3 - - - +
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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