Contacts of the strand formed by residues 122 - 129 (chain A) in PDB entry 2AWP
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 GLY 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A HIS* 3.8 2.5 - - - -
121A SER* 1.3 73.0 - - - +
123A TRP* 1.3 72.0 + - - -
139A THR 3.2 13.2 - - - -
141A ASP 3.7 6.3 - - - -
159A ILE* 3.0 39.1 + - - +
160A TRP* 3.3 14.6 + - - +
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Residues in contact with TRP 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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70A GLN* 3.0 17.4 + - - -
73A ASN* 3.4 51.4 - - + +
74A HIS* 3.5 25.6 - + - -
77A TYR* 3.7 11.7 - - + -
118A HIS* 4.8 1.8 + - - -
122A GLY* 1.3 83.1 - - - -
124A GLY* 1.3 59.5 + - - +
125A TRP* 3.4 23.2 - + + +
138A GLN* 3.3 6.2 - - - +
139A THR* 2.9 41.1 + - - +
141A ASP 2.9 30.3 + - - -
143A GLY 4.1 1.1 - - - -
156A THR* 3.4 17.9 - - + +
157A CYS 3.4 6.3 - - - -
158A ASP* 3.4 47.1 - - + -
159A ILE* 4.0 5.4 - - - +
160A TRP* 3.6 3.4 - - - +
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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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111A PHE* 3.5 10.7 - - - -
114A VAL* 4.9 3.1 - - - -
115A LEU* 3.5 22.6 - - - +
123A TRP* 1.3 74.6 - - - +
125A TRP* 1.3 60.0 + - - -
137A LEU 3.6 6.1 - - - -
138A GLN* 4.4 4.0 - - - -
156A THR* 2.9 19.1 + - - -
157A CYS 2.9 21.3 + - - -
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Residues in contact with TRP 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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72A TRP* 4.0 12.6 - + - -
73A ASN* 3.5 26.0 - - + -
76A PHE* 3.8 15.9 - + - -
111A PHE* 3.4 11.2 - - - -
123A TRP* 3.4 19.2 - + + +
124A GLY* 1.3 75.1 - - - -
126A LEU* 1.3 59.4 + - - +
127A VAL* 3.5 18.2 - - + -
136A ILE* 3.3 7.1 - - - -
137A LEU 2.7 41.7 + - - +
139A THR* 2.9 33.3 + - + +
143A GLY 3.9 4.5 - - - -
144A ASN* 3.4 21.8 - - + -
145A PRO* 3.5 17.5 - - + -
153A PRO* 4.1 13.7 - - + -
155A LEU 3.5 8.7 - - - -
156A THR* 3.3 39.3 - - + -
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Residues in contact with LEU 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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93A ILE* 4.1 16.8 - - + -
97A ILE* 4.7 4.7 - - + -
101A PHE* 4.0 8.3 - - + -
107A PHE* 3.7 40.8 - - + -
111A PHE* 4.2 3.3 - - + -
125A TRP* 1.3 72.8 - - - +
127A VAL* 1.3 57.5 + - - +
134A LEU* 4.0 26.5 - - + -
135A VAL 3.5 14.8 - - - +
136A ILE* 4.9 0.2 - - + -
153A PRO* 3.9 0.5 - - - +
154A ILE* 2.8 55.1 + - + -
155A LEU* 3.0 31.5 + - + +
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Residues in contact with VAL 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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125A TRP* 3.5 24.2 - - + -
126A LEU* 1.3 78.8 - - - +
128A LEU* 1.3 70.9 + - - +
129A ASN 3.9 0.9 - - - +
134A LEU* 3.2 6.1 - - - +
135A VAL* 2.9 55.4 + - + +
137A LEU* 3.8 19.5 - - + -
145A PRO* 3.7 21.5 - - + -
150A THR 4.2 8.3 - - - +
151A GLY* 4.3 1.8 - - - -
152A ILE 3.4 15.3 - - - +
153A PRO* 4.5 3.1 - - + -
154A ILE* 4.0 4.5 - - - -
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Residues in contact with LEU 128 (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 LYS* 3.7 19.7 - - - +
127A VAL* 1.3 72.1 - - - +
129A ASN* 1.3 67.9 + - - +
132A ASN* 3.4 53.4 - - - +
133A LYS 3.7 4.9 - - - +
134A LEU* 4.0 8.5 - - + +
151A GLY* 3.2 0.7 - - - -
152A ILE* 2.8 43.6 + - + +
154A ILE* 3.7 14.5 - - + +
192A LEU* 4.3 5.6 - - + -
195A ALA* 3.6 36.1 - - + +
196A LEU* 4.0 7.4 - - + +
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Residues in contact with ASN 129 (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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127A VAL* 3.6 2.0 + - - -
128A LEU* 1.3 81.2 - - - +
130A ASN* 1.3 61.2 + - - +
131A ASN* 2.8 23.1 + - - +
132A ASN* 3.0 18.0 + - - -
133A LYS* 2.8 39.5 + - - +
135A VAL* 3.5 35.8 - - + +
150A THR 3.7 17.5 - - - +
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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