Contacts of the strand formed by residues 107 - 116 (chain A) in PDB entry 1U1C
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 VAL 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY 3.8 1.3 + - - +
106A ASP* 1.3 75.2 - - - +
108A LEU* 1.3 65.8 - - - +
109A VAL* 5.4 0.4 - - + -
144A ALA* 4.3 4.5 - - + -
149A ALA* 4.1 7.8 - - + +
150A THR 2.9 10.1 + - - +
151A THR* 3.3 30.4 - - + +
152A HIS 3.1 21.8 + - - -
216A VAL* 3.6 24.0 - - + -
217A ALA 3.5 13.5 - - - +
218A GLY* 4.7 2.5 - - - +
240A HIS* 5.9 2.7 - - + -
241A ALA* 4.8 8.5 - - + -
244A ILE* 3.8 30.3 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 4.1 1.3 - - + -
102A ILE* 3.9 14.4 - - + -
106A ASP* 4.8 1.1 - - + -
107A VAL* 1.3 86.3 - - - +
109A VAL* 1.3 62.2 + - - +
110A THR* 4.0 3.7 + - - +
152A HIS* 3.5 36.6 - - + -
193A MET* 3.9 20.2 - - + +
194A ASN* 3.5 43.1 - - + +
215A MET 4.0 0.2 - - - +
216A VAL* 3.3 6.6 - - - +
217A ALA* 2.8 41.2 + - + +
219A VAL* 3.6 24.9 - - + -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 5.4 1.8 - - + -
108A LEU* 1.3 75.9 - - - +
110A THR* 1.3 63.7 + - - +
111A THR 3.7 0.2 + - - -
137A THR* 3.8 32.5 - - + +
140A LEU* 4.2 26.5 - - + +
141A VAL* 3.8 25.1 - - + -
144A ALA* 5.5 0.4 - - + -
151A THR* 4.1 16.6 - - + -
152A HIS 3.1 9.2 + - - +
153A VAL* 3.5 7.6 - - + +
154A GLY 3.3 23.7 + - - +
193A MET* 3.7 2.8 - - - +
215A MET 3.6 9.0 - - - +
216A VAL* 4.2 10.3 - - + -
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.8 3.3 + - - +
109A VAL* 1.3 77.7 - - - +
111A THR* 1.3 59.8 + - - +
112A ALA* 3.4 27.8 - - - +
113A SER* 3.6 11.9 - - - +
132A ALA* 3.4 17.7 - - - +
137A THR* 4.4 2.3 + - - -
154A GLY 3.4 5.6 - - - +
156A THR* 2.6 35.4 + - - +
193A MET* 4.8 0.9 - - - +
194A ASN* 5.1 0.5 + - - -
203A LEU* 4.3 5.4 - - + -
215A MET* 3.1 40.6 + - + +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 1.3 72.6 - - - +
112A ALA* 1.3 62.3 + - - +
131A VAL* 3.4 10.0 - - + +
132A ALA* 2.9 28.4 + - - +
137A THR* 4.7 13.2 - - + +
153A VAL* 3.4 26.0 - - - +
154A GLY* 3.0 17.9 + - - -
111C THR* 5.5 1.3 - - - +
131C VAL* 3.7 23.1 - - + -
132C ALA 4.0 10.8 - - - +
134C PHE* 4.4 16.0 + - + +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.4 5.4 - - - +
111A THR* 1.3 81.0 - - - +
113A SER* 1.3 62.9 + - - +
130A ALA 3.1 14.4 - - - +
131A VAL* 3.9 7.6 - - + +
154A GLY 4.1 0.6 + - - -
155A VAL* 3.3 10.3 - - - +
156A THR 3.2 20.3 + - - -
203A LEU* 4.4 0.7 - - - -
129C PRO* 3.5 25.6 - - + -
131C VAL* 3.6 20.8 - - + +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.6 12.5 - - - +
112A ALA* 1.3 71.8 - - - +
114A VAL* 1.3 66.7 + - - +
115A ARG* 3.5 3.1 + - - +
130A ALA* 2.9 23.9 + - - +
156A THR* 3.1 9.3 + - - -
158A SER* 4.2 0.7 - - - -
199A SER* 2.5 34.3 + - - -
200A ALA* 3.9 20.9 - - - -
203A LEU* 3.9 2.1 - - - +
127C GLU 3.8 2.1 - - - +
129C PRO* 3.4 16.4 - - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 1.3 70.5 - - - +
115A ARG* 1.3 62.1 + - - +
116A LEU* 3.1 28.7 + - + -
155A VAL* 3.7 21.5 - - + +
156A THR 2.7 11.6 + - - +
157A ALA* 3.9 13.2 - - + -
158A SER* 3.0 27.9 + - - +
187A TRP* 3.8 22.2 - - + -
192A VAL* 4.0 12.8 - - + -
127C GLU* 3.4 17.7 - - + +
128C PHE* 3.8 20.2 - - + +
129C PRO* 3.9 1.3 - - + -
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 4.0 1.8 - - - +
114A VAL* 1.3 69.2 - - - +
116A LEU* 1.3 57.6 + - - +
117A ASP* 3.2 17.5 + - - +
120A SER* 2.8 38.4 + - - +
121A LEU* 3.3 13.3 - - - +
124A ALA 2.8 23.6 + - - -
125A PRO 2.8 18.9 + - - -
126A LEU* 3.4 28.8 + - + +
128A PHE* 2.8 37.9 + - - +
130A ALA* 3.7 22.9 - - + +
200A ALA* 4.1 9.9 - - + -
204A THR* 3.8 18.0 - - - +
127C GLU* 2.9 31.8 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.1 15.7 + - + +
115A ARG* 1.3 70.4 - - - +
117A ASP* 1.3 55.6 + - - +
157A ALA* 4.1 19.7 - - + -
158A SER 3.0 20.0 + - - +
159A SER* 3.9 17.9 - - - -
160A ASP 3.0 17.2 + - - -
165A GLY 4.5 1.3 - - - +
179A HIS* 6.0 1.1 - - - +
180A PHE* 4.4 26.5 - - + -
187A TRP* 3.6 43.5 - - + +
195A TYR* 4.4 4.7 - - + -
122B HIS* 3.2 16.3 + - - -
127C GLU* 4.0 15.3 - - + +
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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