Contacts of the strand formed by residues 146 - 154 (chain G) in PDB entry 1LNU
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 PHE 146 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 5.8 0.2 - - + -
13G VAL* 3.8 33.2 - - + -
22G GLN* 5.1 2.0 - - - -
112G ASN 2.9 3.6 + - - -
113G ILE* 2.6 47.2 + - + +
114G PHE* 4.2 13.5 - + - -
116G PRO* 4.2 18.2 - - + -
138G PHE* 3.6 38.1 - + + -
139G PHE 3.0 19.3 - - - +
140G VAL* 4.6 8.5 - - + -
141G ASN* 2.7 16.3 + - - +
144G TYR 3.6 16.6 - - - -
145G SER* 1.3 80.2 - - - +
147G HIS* 1.3 59.2 + - - +
34H VAL* 5.1 2.5 - - + -
36H GLN* 3.3 25.4 - - + -
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Residues in contact with HIS 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLY* 5.3 2.5 + - - -
109G PHE* 3.8 22.3 - + + -
110G VAL 2.9 18.2 - - - +
111G ASP* 2.9 26.0 + - + +
113G ILE* 4.0 4.0 - - - -
138G PHE* 4.7 0.7 - - - -
139G PHE* 2.7 68.3 + + + +
140G VAL 3.8 9.4 - - - -
141G ASN* 2.5 28.4 + - - -
146G PHE* 1.3 71.9 - - - +
148G LYS* 1.3 58.8 + - - +
149G LEU* 4.1 4.7 - - + +
176H ARG* 6.2 1.6 - - - -
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Residues in contact with LYS 148 (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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22G GLN* 5.2 0.2 + - - -
108G CYS 3.8 0.5 - - - +
110G VAL* 2.9 33.8 + - - +
113G ILE* 3.6 14.5 - - + +
118G ILE* 4.5 3.6 - - + -
120G ILE* 3.5 17.7 - - + -
135G GLU* 3.2 34.3 + - + +
136G THR* 2.2 43.9 + - - +
137G SER* 3.9 9.1 - - - +
138G PHE* 3.4 41.2 - - + -
147G HIS* 1.3 73.7 - - - +
149G LEU* 1.3 85.7 + - - +
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Residues in contact with LEU 149 (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 PHE* 5.1 1.6 - - + -
107G ILE* 3.8 25.1 - - + -
108G CYS 3.7 2.5 - - - -
109G PHE* 3.5 37.0 - - + -
120G ILE* 4.8 1.1 - - - -
135G GLU* 3.3 6.9 - - - +
136G THR* 2.8 44.1 + - + +
139G PHE* 3.9 22.2 - - + -
147G HIS* 4.1 7.2 - - + +
148G LYS* 1.3 92.4 - - - +
150G SER* 1.3 60.9 + - - +
151G TYR* 4.0 15.3 - - + +
176H ARG 5.4 0.9 - - - +
177H ASN* 4.3 9.2 - - - +
178H GLY* 4.2 10.1 - - - +
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Residues in contact with SER 150 (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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106G LEU 3.8 0.2 - - - +
107G ILE* 3.5 5.9 - - - +
108G CYS* 3.0 38.4 + - - -
120G ILE* 4.3 31.7 + - - +
122G TRP* 3.2 22.6 + - - -
133G VAL* 4.1 5.2 - - - +
134G TYR 3.2 10.0 + - - -
135G GLU* 4.2 7.1 + - - +
149G LEU* 1.3 74.8 - - - +
151G TYR* 1.3 68.1 + - - +
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Residues in contact with TYR 151 (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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45G MET* 5.3 1.6 - - + -
95G LYS* 6.4 0.7 - - + -
105G THR* 3.7 17.3 - - + -
106G LEU 3.5 3.6 - - - -
107G ILE* 3.4 33.2 - - + -
122G TRP* 3.2 7.3 + - - -
132G GLY 3.7 1.0 - - - +
133G VAL* 3.2 7.1 - - - +
134G TYR* 2.5 69.8 + + + +
136G THR* 3.4 26.4 - - + +
149G LEU* 4.0 9.0 - - + +
150G SER* 1.3 76.7 + - - +
152G LEU* 1.3 58.8 + - - +
153G THR* 4.0 0.9 - - - +
177H ASN 2.4 33.4 + - - -
178H GLY* 3.1 21.8 - - - -
179H ASP* 3.3 18.3 + - + +
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Residues in contact with LEU 152 (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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105G THR* 3.3 5.0 - - - +
106G LEU* 2.8 44.6 + - + +
122G TRP* 3.1 56.1 - - + +
124G ARG* 4.4 8.5 - - - +
129G VAL* 5.3 6.7 - - + -
131G ASP 5.6 2.7 - - - +
132G GLY 4.0 1.3 - - - -
133G VAL* 4.7 5.2 - - + +
151G TYR* 1.3 71.6 - - - +
153G THR* 1.3 68.7 + - - +
154G PHE* 3.2 30.5 + - + -
162G TYR* 3.8 28.9 - - + -
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Residues in contact with THR 153 (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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103G PRO* 6.0 4.5 - - + -
104G ASN 3.8 7.2 - - - +
105G THR* 4.4 12.7 + - - +
124G ARG* 4.6 4.0 + - - -
131G ASP 4.8 2.3 - - - +
132G GLY* 2.9 34.3 + - - +
151G TYR* 4.0 0.7 - - - +
152G LEU* 1.3 79.3 - - - +
154G PHE* 1.3 62.5 + - - +
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Residues in contact with PHE 154 (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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94G PRO* 5.4 1.8 - - + -
98G VAL* 5.7 2.2 - - + -
103G PRO* 3.8 4.7 - - - +
104G ASN* 3.0 75.6 + - + +
105G THR 3.9 1.6 - - - -
106G LEU* 3.6 24.5 - - + -
124G ARG* 4.1 8.1 - - - +
152G LEU* 3.2 26.2 - - + -
153G THR* 1.3 72.9 - - - +
155G ILE* 1.3 75.1 + - - +
156G PRO* 3.7 21.3 - - + -
162G TYR* 2.8 43.7 - + - +
179G TRP* 3.5 28.7 - + - -
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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