Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 2AGA
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 2.7 35.2 - - + +
24A LEU* 5.8 0.2 - - + -
79A PHE* 3.9 21.7 - + - -
80A PHE 3.1 20.6 + - - -
82A ILE* 3.1 28.8 - - + +
85A ILE* 3.0 37.2 - - + -
118A ILE* 2.9 40.4 - - + -
119A CYS 3.1 14.6 - - - +
120A ASN* 3.4 23.6 - - + +
123A GLU 4.3 2.0 - - - -
124A HIS* 1.3 80.3 - + - +
126A PHE* 1.3 69.5 + - - +
127A THR* 3.7 20.0 - - + -
139A ASN* 2.8 27.0 + - - -
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Residues in contact with PHE 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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118A ILE* 2.9 7.4 - - - +
119A CYS* 2.5 61.2 + - + +
121A TYR* 3.3 46.2 - + + -
124A HIS* 4.1 10.3 - + + -
125A TRP* 1.3 86.4 - - - +
127A THR* 1.3 64.0 + - - +
128A VAL* 5.0 0.4 - - - -
137A ASN* 3.5 23.1 - - - +
139A ASN* 3.5 26.5 - - + +
141A LEU* 2.9 38.6 - - + -
156A PHE* 5.3 4.5 - + - -
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Residues in contact with THR 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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20A ALA* 4.8 1.9 + - - +
23A CYS* 2.8 38.0 - - + +
24A LEU* 5.0 1.8 - - - +
27A LEU* 4.7 19.3 - - + -
85A ILE* 5.6 1.3 - - + -
116A SER* 5.6 0.9 - - - +
117A PHE 4.1 1.1 - - - +
118A ILE* 3.6 29.8 - - + -
125A TRP* 3.7 16.7 - - + -
126A PHE* 1.3 74.2 - - - +
128A VAL* 1.3 65.6 + - - +
129A ARG* 5.5 0.4 - - - +
138A LEU* 2.8 39.1 + - - +
139A ASN* 5.2 0.7 + - - -
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Residues in contact with VAL 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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27A LEU* 5.0 0.8 - - - +
116A SER* 3.4 7.3 + - - -
117A PHE* 2.5 57.2 + - + +
118A ILE 4.8 0.2 - - - -
119A CYS* 4.6 17.0 - - + +
126A PHE 4.8 0.2 - - - +
127A THR* 1.3 78.9 - - - +
129A ARG* 1.3 62.6 + - - +
135A TRP* 3.8 29.2 - - + -
136A PHE 3.5 17.0 - - - +
137A ASN* 3.9 24.0 - - - +
148A ILE* 4.6 3.4 - - + -
153A LEU* 4.3 12.6 - - + -
156A PHE* 4.9 6.1 - - + -
157A LEU* 5.8 1.1 - - + -
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Residues in contact with ARG 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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9A ILE* 4.9 7.5 - - - +
10A PHE* 5.0 7.9 + - - +
23A CYS 5.5 0.4 + - - -
26A ASN* 4.8 9.6 + - - +
27A LEU* 4.0 47.2 - - + +
115A ARG* 4.2 22.9 - - - +
116A SER* 4.6 0.4 - - - +
127A THR 4.1 1.5 + - - +
128A VAL* 1.3 75.6 - - - +
130A LYS* 1.3 65.4 + - - +
131A LEU* 3.2 17.3 + - - +
135A TRP* 4.1 2.5 - - - -
136A PHE* 2.8 42.8 + - - +
138A LEU* 4.5 29.5 - - - +
175A PRO 5.8 0.2 - - - -
177A CYS* 3.8 22.0 - - - -
179A ALA* 3.7 24.0 - - - +
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Residues in contact with LYS 130 (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 ILE 3.6 8.5 + - - -
113A ASN 5.1 1.6 + - - -
114A GLU 3.1 28.0 + - - +
115A ARG* 2.7 52.3 + - + +
129A ARG* 1.3 74.8 + - - +
131A LEU* 1.3 59.5 + - - +
132A GLY 3.8 11.5 + - - +
133A LYS* 4.6 12.1 - - + +
134A GLN* 3.3 23.1 - - - +
135A TRP* 3.6 24.6 - - + +
150A ASP* 5.6 4.3 + - - -
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Residues in contact with LEU 131 (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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5A SER* 4.6 7.2 - - - +
9A ILE* 3.6 33.2 - - + -
129A ARG* 3.2 10.6 + - - +
130A LYS* 1.3 69.6 - - - +
132A GLY* 1.3 65.0 + - - +
133A LYS 2.9 6.9 + - - -
134A GLN* 2.6 25.4 + - + +
136A PHE* 3.1 52.9 - - + -
179A ALA* 2.9 44.2 - - + +
182A LEU* 4.6 2.0 - - + -
183A LEU* 6.1 0.4 - - - +
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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