Contacts of the strand formed by residues 117 - 127 (chain A) in PDB entry 1A8H
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 ILE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.8 8.5 - - + +
111A VAL* 3.9 16.5 + - + -
112A TYR* 3.7 43.1 - - + +
115A GLY* 3.2 8.2 - - - +
116A ASP* 1.3 86.2 - - - +
118A TYR* 1.3 66.2 + - - +
159A TYR* 4.1 18.8 - - + -
160A PHE 3.1 13.0 - - - +
161A PHE* 4.6 4.9 - - + -
162A ARG* 4.8 1.2 + - - -
203A ILE* 4.2 13.7 - - + -
218A TRP* 3.5 43.1 - - + -
228A PHE* 5.5 2.0 - - + -
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Residues in contact with TYR 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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112A TYR* 6.0 0.4 - - - -
117A ILE* 1.3 75.8 - - - +
119A TYR* 1.3 72.0 + - - +
120A GLY* 4.6 4.3 - - - -
159A TYR* 3.4 7.9 - - - -
160A PHE* 2.7 72.8 + + + +
162A ARG* 3.7 48.5 - - + +
200A ASP* 2.4 40.9 + - - +
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Residues in contact with TYR 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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118A TYR* 1.3 84.5 - - - +
120A GLY* 1.3 66.5 + - - +
121A GLU* 5.7 3.1 - - + -
157A GLY* 3.1 38.2 + - - -
158A ASN 3.7 8.1 - - - -
159A TYR* 3.7 34.8 - + + -
219A ASP* 5.5 0.7 - - - -
222A HIS* 4.1 17.9 + + - -
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Residues in contact with GLY 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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118A TYR* 3.8 7.5 + - - -
119A TYR* 1.3 82.9 - - - +
121A GLU* 1.3 65.9 + - - +
157A GLY* 3.5 6.4 - - - -
158A ASN 2.8 32.6 + - - -
160A PHE* 3.6 9.1 - - - -
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Residues in contact with GLU 121 (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 TYR* 5.7 3.8 - - + -
120A GLY* 1.3 78.8 - - - +
122A TYR* 1.3 63.2 + - - +
123A GLU* 4.2 1.1 + - + +
155A LYS* 3.1 37.1 - - + +
156A GLU 3.6 8.7 + - - +
157A GLY* 4.8 3.8 + - - -
160A PHE* 3.6 12.3 - - - -
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Residues in contact with TYR 122 (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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121A GLU* 1.3 74.3 - - - +
123A GLU* 1.3 76.8 + - - +
124A GLY* 4.9 1.1 - - - -
133A PHE* 3.6 48.8 - + + +
135A THR* 5.7 4.7 - - - +
154A ARG 3.6 0.9 - - - +
155A LYS* 3.0 6.6 - - - -
156A GLU 2.9 32.9 + - - +
158A ASN* 3.7 21.8 - - - +
160A PHE* 4.0 22.4 - + + -
202A SER* 4.2 14.1 - - - -
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Residues in contact with GLU 123 (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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121A GLU* 4.2 1.5 + - + +
122A TYR* 1.3 95.8 - - - +
124A GLY* 1.3 61.5 + - - +
153A ARG* 3.5 34.6 + - - +
154A ARG 3.2 14.0 + - - +
155A LYS* 4.7 8.3 - - + -
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Residues in contact with GLY 124 (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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122A TYR* 4.9 1.6 - - - -
123A GLU* 1.3 80.9 - - - +
125A LEU* 1.3 67.2 + - - -
126A TYR 3.4 0.2 + - - -
133A PHE* 3.6 9.1 - - - -
134A TYR 5.5 0.7 - - - -
153A ARG* 3.4 23.7 - - - -
154A ARG 2.9 30.4 + - - +
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Residues in contact with LEU 125 (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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124A GLY* 1.3 71.0 - - - -
126A TYR* 1.3 58.8 + - - +
133A PHE* 3.2 9.2 - - - -
134A TYR* 2.9 49.5 + - + +
135A THR* 4.0 6.7 - - - -
136A GLU* 3.3 33.7 - - - +
139A LEU* 3.4 19.7 - - + -
151A VAL* 3.8 27.8 - - + +
152A GLU 3.8 3.1 - - - -
153A ARG* 4.7 24.4 - - + +
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Residues in contact with TYR 126 (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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124A GLY 4.1 0.9 - - - +
125A LEU* 1.3 75.8 - - - +
127A CYS* 1.3 75.3 + - - +
128A VAL* 4.0 8.3 + - + +
131A GLU* 3.2 24.4 + - - -
132A ARG 3.6 15.3 - - - -
133A PHE* 3.6 29.4 - + + -
151A VAL* 3.3 6.8 - - - -
152A GLU* 2.8 43.4 + - - +
154A ARG* 3.7 38.2 - - + -
156A GLU* 4.4 2.7 - - + -
205A ARG* 3.3 19.7 - - - -
209A ARG* 3.2 40.8 - - - +
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Residues in contact with CYS 127 (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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126A TYR* 1.3 75.5 - - - +
128A VAL* 1.3 52.7 + - - +
129A SER 3.5 4.3 - - - -
130A CYS* 3.3 15.9 + - + -
131A GLU* 2.7 34.8 + - - -
132A ARG 3.3 7.4 + - - -
134A TYR* 4.0 8.9 - - + -
144A CYS* 3.8 1.6 - - - -
147A HIS* 3.7 2.2 - - - -
149A ARG* 3.5 27.1 - - - +
150A PRO 5.4 0.2 - - - -
151A VAL* 3.9 16.3 - - + +
1000A ZN 2.3 36.8 - - - -
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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