Contacts of the strand formed by residues 145 - 153 (chain G) in PDB entry 1U3H
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 145 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12G VAL* 3.9 21.8 - - + -
111G ASN 3.4 4.7 + - - -
112G ILE* 2.7 51.2 + - + +
113G PHE* 4.1 3.1 - + - -
115G PRO* 3.1 37.5 - - + -
137G PHE* 3.9 33.7 - - + -
138G PHE 3.0 23.1 - - - +
139G VAL* 4.3 10.5 - - + -
140G ASN* 3.2 8.5 - - - +
143G TYR 3.7 12.8 - - - -
144G SER* 1.3 80.3 - - - +
146G HIS* 1.3 59.3 + - - +
10H GLN* 3.4 38.1 - - + -
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Residues in contact with HIS 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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28G GLY 5.4 1.6 + - - -
108G PHE* 3.5 27.5 - + + -
109G VAL 2.9 17.0 - - - +
110G ASP* 3.6 15.9 - - - +
112G ILE* 3.9 1.8 - - - -
137G PHE 3.7 0.9 - - - -
138G PHE* 2.8 62.2 + + + +
139G VAL 4.0 7.4 - - - -
140G ASN* 2.6 27.8 + - - -
145G PHE* 1.3 76.3 - - - +
147G LYS* 1.3 60.5 + - - +
148G LEU* 4.3 8.2 - - + +
149H ARG* 5.4 8.1 - - - -
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Residues in contact with LYS 147 (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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107G CYS 3.8 0.7 - - - +
108G PHE* 4.5 0.5 - - - -
109G VAL* 3.0 31.4 + - - +
112G ILE* 3.7 13.4 - - + +
117G ILE* 4.3 4.9 + - + +
119G ILE* 4.0 15.5 - - + -
134G GLU* 3.0 36.4 + - + -
135G THR* 3.3 24.7 + - - +
136G SER* 3.6 10.8 - - - +
137G PHE* 3.4 49.8 - - + -
146G HIS* 1.3 76.3 - - - +
148G LEU* 1.3 75.1 + - - +
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Residues in contact with LEU 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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92G PHE* 4.8 0.9 - - + -
106G ILE* 3.9 16.8 - - + -
107G CYS 3.2 5.8 - - - +
108G PHE* 4.0 21.1 - - + -
119G ILE* 5.4 0.7 - - - -
134G GLU* 3.4 3.5 - - - +
135G THR* 2.8 46.8 + - + +
138G PHE* 3.9 26.5 - - + -
146G HIS* 4.3 12.6 - - + +
147G LYS* 1.3 84.9 - - - +
149G SER* 1.3 60.1 - - - +
150G TYR* 3.9 7.6 - - + +
149H ARG* 4.0 11.2 - - + +
150H ASN 3.6 27.1 - - - +
151H GLY* 4.5 7.9 - - - -
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Residues in contact with SER 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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106G ILE* 3.5 3.3 - - - +
107G CYS* 2.8 35.5 + - - -
119G ILE* 3.6 35.5 + - - +
121G TRP* 3.0 24.8 + - - -
132G VAL* 4.1 6.1 - - - +
133G TYR 3.4 11.4 + - - -
134G GLU* 4.2 9.2 + - - +
148G LEU* 1.3 75.2 - - - +
150G TYR* 1.3 63.3 + - - +
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Residues in contact with TYR 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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94G LYS* 6.1 1.1 - - + -
104G THR* 3.7 17.9 - - + -
105G LEU 3.3 3.1 - - - -
106G ILE* 3.6 33.2 - - + -
121G TRP* 3.8 3.6 - - - +
131G GLY 3.2 1.4 - - - +
132G VAL* 3.1 10.7 - - - +
133G TYR* 2.7 69.1 + + + +
135G THR* 3.5 27.2 - - + +
148G LEU* 3.9 9.7 - - + +
149G SER* 1.3 76.7 + - - +
151G LEU* 1.3 60.6 + - - +
152G THR* 4.1 1.6 - - + +
150H ASN 2.5 29.8 + - - -
151H GLY* 3.2 20.4 + - - -
152H ASP* 4.7 11.7 - - + -
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Residues in contact with LEU 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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104G THR* 4.2 1.6 - - - -
105G LEU* 2.8 38.5 + - + +
121G TRP* 3.6 37.9 - - + +
123G ARG* 4.9 3.1 - - - +
128G VAL* 3.7 33.2 - - + -
130G ASP 3.9 4.0 - - - +
131G GLY 3.2 12.1 - - - +
132G VAL* 3.7 9.9 - - + -
150G TYR* 1.3 74.9 - - - +
152G THR* 1.3 75.2 + - - +
153G PHE* 3.5 3.8 + - + -
161G TYR* 3.5 38.6 - - + -
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Residues in contact with THR 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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103G ASN 3.4 11.0 - - - -
104G THR* 4.2 13.9 - - + +
123G ARG* 5.4 2.4 + - - -
130G ASP 5.2 0.3 - - - +
131G GLY* 2.9 30.7 + - - +
150G TYR* 5.6 1.6 - - + +
151G LEU* 1.3 85.2 - - - +
153G PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 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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93G PRO* 5.0 1.8 - - + -
97G VAL* 4.5 5.8 - - + -
102G PRO* 3.6 2.4 - - - +
103G ASN* 2.9 52.3 + - + -
104G THR 3.8 2.5 - - - -
105G LEU* 3.7 25.8 - - + -
123G ARG* 5.5 2.5 - - - +
151G LEU* 3.7 13.9 - - + +
152G THR* 1.3 77.3 - - - +
154G ILE* 1.3 72.4 + - - +
155G PRO* 3.6 32.3 - - + +
161G TYR* 3.5 41.3 - + + +
178G TRP* 4.1 33.2 - + - -
180G PRO* 5.9 1.8 - - + -
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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