Contacts of the strand formed by residues 118 - 123 (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 ASN 118 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116G VAL* 6.1 1.4 - - - +
117G ILE* 1.3 86.4 + - - +
119G ILE* 1.3 64.2 + - - +
120G THR* 4.1 8.2 + - + -
164G LYS 3.5 3.3 - - - +
165G VAL* 3.6 1.6 - - - -
166G GLU* 3.0 59.5 + - + +
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Residues in contact with ILE 119 (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* 4.5 1.3 - - - -
109G VAL* 3.7 27.6 - - + -
117G ILE* 4.1 19.2 + - + -
118G ASN* 1.3 76.4 - - - +
120G THR* 1.3 70.8 + - - +
121G TRP* 5.1 0.8 - - - +
132G VAL* 5.6 3.8 - - - +
134G GLU* 3.9 20.7 + - - +
147G LYS* 4.0 34.5 - - + +
149G SER* 3.6 31.0 + - - +
163G CYS* 3.8 26.0 - - - -
164G LYS 3.4 3.1 - - - +
165G VAL* 4.6 3.8 - - + -
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Residues in contact with THR 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ASN* 4.9 8.9 + - + -
119G ILE* 1.3 82.2 - - - +
121G TRP* 1.3 71.8 + - - +
122G LEU* 5.6 1.8 - - - +
127G SER* 5.6 4.7 - - - -
128G VAL 6.0 0.7 - - - -
132G VAL* 6.3 0.7 - - - -
163G CYS* 3.6 6.1 - - - -
164G LYS* 2.7 57.7 + - - +
166G GLU* 5.9 2.8 - - - +
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Residues in contact with TRP 121 (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 VAL* 4.5 6.3 - - + -
105G LEU* 3.7 42.4 - - + -
106G ILE 3.9 3.8 - - - -
107G CYS* 3.5 37.7 - - + -
119G ILE* 5.1 0.2 - - - +
120G THR* 1.3 84.8 - - - +
122G LEU* 1.3 67.1 + - - +
127G SER* 3.5 7.1 + - - -
128G VAL* 3.0 37.4 + - + +
132G VAL* 3.7 27.1 - - + +
149G SER* 3.0 34.6 + - - -
150G TYR 3.8 4.4 - - - -
151G LEU* 3.6 35.5 - - + +
161G TYR* 4.9 1.6 - - + -
162G ASP 3.5 20.4 - - - -
163G CYS* 4.1 14.4 - - + -
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Residues in contact with LEU 122 (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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129C ALA* 4.4 11.7 - - + -
120G THR* 5.6 1.8 - - - +
121G TRP* 1.3 84.3 - - - +
123G ARG* 1.3 59.8 + - - +
124G ASN 4.0 0.4 - - - -
125G SER* 4.2 15.9 - - - +
126G LYS 3.1 8.5 - - - +
127G SER* 3.7 24.7 - - - +
128G VAL* 4.1 1.8 - - - -
161G TYR* 3.3 10.7 - - - +
162G ASP* 2.8 54.8 + - + +
164G LYS* 4.8 16.6 - - + +
175G LEU* 4.2 27.4 - - + -
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Residues in contact with ARG 123 (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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122G LEU* 1.3 71.6 - - - +
124G ASN* 1.3 89.6 + - - +
126G LYS* 2.7 24.0 + - - +
128G VAL* 3.4 37.9 - - + +
151G LEU* 4.9 4.0 - - - +
152G THR 5.4 3.4 + - - -
153G PHE* 5.5 1.4 - - - +
159G ASP* 4.0 18.8 - - - +
160G ILE 3.6 3.4 - - - +
161G TYR* 3.2 33.5 + - + -
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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