Contacts of the strand formed by residues 108 - 120 (chain A) in PDB entry 1ASZ
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 GLU 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASP 3.5 3.8 + - - +
107A LYS* 1.3 69.3 - - - +
109A VAL* 1.3 59.4 + - - +
169A ARG* 2.8 36.1 + - + +
170A GLY 3.0 19.7 - - - +
171A ILE* 4.1 16.9 - - + +
192A THR* 4.9 3.5 - - - +
193A LYS* 4.5 13.9 + - - -
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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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94A VAL* 3.9 23.6 - - + -
99A LEU* 5.0 3.4 - - + -
104A ASP* 4.5 10.8 - - - +
107A LYS* 3.2 21.9 + - + +
108A GLU* 1.3 75.5 - - - +
110A LEU* 1.3 62.0 + - - +
111A PHE* 3.8 25.8 - - + -
168A VAL 4.6 0.2 - - - -
169A ARG* 3.4 9.9 - - - +
170A GLY 2.8 35.2 + - - +
172A VAL* 3.8 24.9 - - + -
189A ILE* 4.4 5.4 - - + -
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Residues in contact with LEU 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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91A GLN* 4.6 13.5 - - + +
92A LYS 4.0 12.7 + - - +
93A ARG* 3.1 39.0 - - + +
94A VAL* 2.8 27.2 + - - +
109A VAL* 1.3 75.2 - - - +
111A PHE* 1.3 62.6 + - - +
167A LEU* 3.3 29.2 - - + -
168A VAL 3.4 13.0 - - - +
169A ARG* 3.4 45.8 - - + +
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Residues in contact with PHE 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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93A ARG* 4.2 9.9 - - - -
94A VAL* 3.4 23.8 - - + +
96A PHE* 3.5 29.6 - + + -
99A LEU* 5.7 0.4 - - + -
109A VAL* 3.8 21.3 - - + -
110A LEU* 1.3 76.2 - - - +
112A ARG* 1.3 65.4 + - - +
113A ALA* 4.7 0.9 - - + -
130A LEU* 3.4 32.1 - - + -
132A GLN* 4.1 4.3 - - - +
137A ILE* 5.5 0.2 - - + -
167A LEU* 3.3 5.4 - - - +
168A VAL* 2.7 70.1 + - + +
170A GLY 5.2 0.7 - - - -
189A ILE* 3.4 36.6 - - + -
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Residues in contact with ARG 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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93A ARG* 3.9 16.2 - - + +
94A VAL 5.1 0.2 + - - -
111A PHE* 1.3 76.5 - - - +
113A ALA* 1.3 73.4 + - - +
132A GLN* 3.1 23.3 + - - +
165A ILE* 3.6 18.7 - - + +
166A VAL 3.2 8.7 - - - +
167A LEU* 4.1 2.2 - - - +
197A ILE* 3.3 30.0 - - + +
315B GLU* 3.5 28.2 + - - -
346B ALA* 5.0 6.9 + - - +
347B PHE 4.4 10.2 + - - -
348B GLU* 2.7 47.5 + - - +
520B PRO* 3.3 30.8 - - - +
521B PRO* 5.7 0.4 - - - +
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Residues in contact with ALA 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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96A PHE* 4.2 15.5 - - + -
111A PHE* 4.4 3.1 - - + -
112A ARG* 1.3 83.4 - - - +
114A ARG* 1.3 68.7 + - - +
130A LEU* 4.3 14.6 - - + -
131A ARG 3.2 17.7 - - - +
132A GLN* 4.6 2.9 - - + +
165A ILE* 3.3 4.5 - - - -
166A VAL* 2.6 43.2 + - + +
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Residues in contact with ARG 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 ALA* 1.3 78.7 - - - +
115A VAL* 1.3 60.2 - - - +
116A HIS 3.5 0.4 - - - -
130A LEU* 3.6 6.7 - - - +
131A ARG* 2.8 61.3 + - + +
132A GLN* 6.2 0.2 - - - -
163A GLU* 3.2 29.4 + - - +
164A SER 3.2 4.7 - - - +
165A ILE* 3.2 25.8 - - + +
166A VAL* 5.5 0.2 - - - -
240A ARG* 2.6 41.5 - - - +
311B VAL 3.7 6.1 + - - -
313B ASP* 2.9 29.3 + - - +
517B TYR 3.4 4.8 + - - -
518B GLY 2.7 31.7 + - - -
519B CYS* 3.4 3.8 - - - +
520B PRO* 4.5 2.2 - - - +
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Residues in contact with VAL 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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114A ARG* 1.3 69.1 - - - +
116A HIS* 1.3 63.3 + - - +
117A ASN 4.5 0.9 - - - +
118A THR* 4.1 12.3 - - + -
128A LEU* 4.4 17.5 - - + -
129A THR 4.2 2.2 - - - -
130A LEU* 4.5 7.2 - - + -
160A LEU* 3.8 27.4 - - + +
161A ASN 3.4 24.2 - - - +
162A LEU* 3.5 14.7 - - + +
163A GLU* 2.9 22.5 + - - +
164A SER 2.8 13.6 + - - +
166A VAL* 4.3 21.8 - - + -
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Residues in contact with HIS 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 ARG 3.3 2.8 + - - -
115A VAL* 1.3 73.4 - - - +
117A ASN* 1.3 63.2 + - + +
129A THR* 2.9 28.6 + - + +
131A ARG* 3.5 46.1 + - + +
136A LEU* 3.1 33.2 - - + +
162A LEU* 2.9 17.0 - - - +
163A GLU* 4.5 2.8 - - - +
208A LEU* 4.4 20.5 - - + +
209A GLU* 3.9 25.9 + - + -
212A SER* 5.3 5.2 + - - -
242A VAL* 5.8 4.3 - - + -
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Residues in contact with ASN 117 (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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115A VAL* 3.5 0.7 - - - +
116A HIS* 1.3 89.7 - - + +
118A THR* 1.3 74.3 + - - +
119A ARG* 2.8 39.5 - - - +
128A LEU* 3.7 0.3 - - - +
129A THR* 2.8 40.1 + - + +
162A LEU* 3.4 14.2 - - - +
209A GLU* 5.3 10.8 - - + +
626R G 5.7 0.7 + - - -
638R C 3.8 15.6 + - - -
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Residues in contact with THR 118 (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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115A VAL* 4.1 20.6 - - + -
117A ASN* 1.3 91.9 + - - +
119A ARG* 1.3 63.5 + - - +
127A PHE 3.5 5.6 - - - -
128A LEU* 3.2 28.9 - - + -
157A ALA 4.1 5.4 - - - +
158A GLY* 3.4 24.7 + - - +
159A SER 5.3 0.2 - - - -
160A LEU 4.1 8.0 + - - +
162A LEU* 4.3 6.4 - - - +
627R G 5.8 0.2 + - - -
638R C 5.2 0.3 + - - -
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Residues in contact with ARG 119 (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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117A ASN* 2.8 26.0 - - - +
118A THR* 1.3 75.4 + - - +
120A GLN* 1.3 55.7 + - - +
121A GLN* 4.5 2.9 - - - +
127A PHE* 2.7 66.1 + - + +
128A LEU 4.8 0.4 - - - +
129A THR* 4.4 11.7 + - - -
181A SER* 4.6 5.1 + - - -
635R U 3.7 26.2 + - - +
636R C 3.0 38.6 + - - -
638R C 2.6 52.1 + - + +
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Residues in contact with GLN 120 (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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119A ARG* 1.3 73.8 - - - +
121A GLN* 1.3 69.4 + - - +
122A GLY 4.9 0.6 - - - +
123A ALA* 5.1 9.5 - - - +
125A LEU 4.0 3.4 - - - +
126A ALA* 3.9 19.4 - - + +
154A VAL* 4.8 3.8 - - - +
155A LYS* 4.2 28.6 - - - +
158A GLY* 3.7 21.0 - - - +
159A SER* 3.5 21.0 + - - -
632R PSU 3.5 22.6 + - - +
638R C 3.1 15.8 + - - +
639R G 5.0 0.7 - - - +
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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