Contacts of the strand formed by residues 128 - 136 (chain C) in PDB entry 1U5D
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 TRP 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C GLU* 3.7 31.0 - - + +
116C LYS 3.6 5.8 - - - -
117C LYS* 3.5 47.0 - - + +
127C GLU* 1.3 80.7 + - - +
129C GLN* 1.3 61.0 + - - +
130C LYS 4.3 0.4 - - - -
168C LEU* 3.6 27.3 + - + -
169C ARG* 3.5 45.4 - - - +
177C CYS* 4.6 0.2 - - - -
189C GLU* 3.5 27.1 - - + -
190C PHE 3.7 14.8 - - - -
191C THR* 3.4 21.8 - - - -
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Residues in contact with GLN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLU* 4.1 2.7 - - - +
116C LYS* 2.9 35.4 + - + +
118C SER* 3.4 25.7 - - - -
127C GLU* 3.7 16.8 - - + +
128C TRP* 1.3 77.7 - - - +
130C LYS* 1.3 64.3 + - - +
131C ARG* 3.4 41.0 + - + +
1003C SO4 4.2 9.2 + - - -
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Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.6 51.7 - - + -
114C LEU 3.5 7.9 - - - +
115C GLU* 4.2 13.0 + - + +
128C TRP 4.4 0.2 + - - -
129C GLN* 1.3 71.2 - - - +
131C ARG* 1.3 81.2 + - - +
144C ALA 3.4 10.1 - - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.3 7.2 - - - -
114C LEU 2.8 35.0 + - - +
116C LYS* 4.1 17.2 - - + +
129C GLN* 3.4 45.8 + - - +
130C LYS* 1.3 93.2 + - - +
132C TRP* 1.3 60.2 + - - +
133C CYS* 3.5 17.3 + - - -
142C TYR* 4.2 11.9 - - + -
143C TYR 3.2 24.0 - - - +
144C ALA* 3.9 14.0 + - - +
152C LYS* 3.9 16.3 - - - +
1003C SO4 2.8 41.7 + - - +
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Residues in contact with TRP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN* 3.1 42.4 + - + -
112C GLY* 3.7 22.9 - - - -
113C TYR* 3.6 47.1 - + + -
131C ARG* 1.3 69.4 - - - +
133C CYS* 1.3 59.5 + - - +
134C VAL* 3.8 17.8 - - + +
142C TYR* 3.2 2.4 - - - -
143C TYR* 2.8 46.1 + + + +
144C ALA 4.1 0.4 + - - -
145C ASN 3.8 6.3 - - - +
146C GLU* 3.5 67.2 - - + +
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Residues in contact with CYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN* 3.1 6.4 - - - +
112C GLY 2.9 35.3 + - - +
114C LEU* 3.9 26.2 - - + -
131C ARG* 3.7 22.0 - - - -
132C TRP* 1.3 74.4 + - - +
134C VAL* 1.3 63.7 + - - +
140C PHE* 3.7 18.4 - - + -
141C TYR 3.6 3.8 - - - -
142C TYR* 3.8 15.7 - - - -
190C PHE* 4.0 15.7 - - - -
201C TRP* 3.6 4.6 - - + -
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 4.0 29.2 - - + -
110C LYS 3.6 3.6 - - - -
111C GLN* 4.1 7.4 - - + +
132C TRP* 3.8 24.0 - - + +
133C CYS* 1.3 80.5 - - - +
135C VAL* 1.3 63.6 + - - +
136C SER* 4.3 3.6 - - - +
139C LEU 3.9 0.5 - - - +
140C PHE* 3.3 8.6 - - - -
141C TYR* 2.8 84.3 + - + +
143C TYR* 4.4 4.3 - - + -
201C TRP* 4.9 0.2 - - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 3.8 1.9 - - - +
109C ILE* 2.9 31.5 + - + +
110C LYS* 2.9 31.4 + - + +
134C VAL* 1.3 74.9 - - - +
136C SER* 1.3 72.1 + - - +
139C LEU 3.4 11.9 - - - +
140C PHE* 4.0 20.9 - - + -
157C ILE* 4.7 7.6 - - + -
201C TRP* 4.0 13.4 - - + -
204C GLN* 5.6 1.3 - - + -
205C ILE* 4.2 18.8 - - + -
208C LEU* 3.8 14.6 - - + -
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C SER* 3.1 35.3 + - - -
108C VAL* 3.7 11.4 + - - +
109C ILE* 4.2 5.6 - - - -
134C VAL* 4.1 1.0 - - - +
135C VAL* 1.3 81.9 - - - +
137C ARG* 1.3 71.3 + - - +
138C GLY 3.0 4.0 + - - -
139C LEU* 2.9 26.3 + - - +
141C TYR* 4.2 16.6 + - - -
208C LEU* 3.8 2.4 - - - +
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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