Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 2AG1
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL 3.0 8.3 + - - +
96A LEU* 3.8 5.5 - - + -
97A PHE* 2.8 31.6 + - - +
126A THR* 4.2 3.1 - - - -
127A LYS* 4.4 2.5 - - + -
128A TRP* 3.3 29.4 - - + +
145A ALA* 3.6 47.6 - - + +
148A ALA* 3.9 11.0 - - + -
149A ALA* 3.7 20.4 - - + +
155A GLY 4.4 0.2 - - - +
156A PRO* 1.3 80.2 - - - +
158A LEU* 1.3 69.4 + - - +
159A LEU* 4.1 0.4 + - + -
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Residues in contact with LEU 158 (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 VAL* 6.1 0.4 - - + -
78A PHE* 3.8 26.0 - - + -
85A ILE* 4.2 4.9 - - + -
97A PHE* 3.7 25.8 - - + +
99A THR* 3.7 28.7 - - + -
118A GLN 4.2 8.3 - - - +
119A VAL* 4.4 19.5 - - + -
122A ALA* 3.9 23.6 - - + -
126A THR* 3.9 5.0 - - + +
128A TRP* 3.0 8.7 + - - +
129A ALA* 3.3 13.0 - - + -
130A HIS* 3.1 24.6 + - - +
157A VAL* 1.3 78.2 - - - +
159A LEU* 1.3 60.9 + - - +
160A ASP* 4.4 3.8 - - + -
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Residues in contact with LEU 159 (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 LEU* 4.2 4.9 - - + +
97A PHE 2.9 9.1 + - - +
98A LEU* 3.6 19.9 - - + -
99A THR* 2.8 28.4 + - - +
128A TRP* 4.7 10.5 - - + -
130A HIS* 3.6 23.8 - - + +
132A VAL* 3.6 21.8 - - + -
138A ILE 5.2 0.2 - - - +
141A LEU* 4.3 6.1 - - + +
142A VAL* 3.7 41.1 - - + +
145A ALA* 4.2 15.5 - - + -
157A VAL 4.1 0.6 + - - -
158A LEU* 1.3 75.3 - - - +
160A ASP* 1.3 61.5 + - - +
161A LEU* 3.8 19.4 + - + +
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Residues in contact with ASP 160 (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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99A THR* 3.6 10.9 - - + +
101A SER* 2.7 30.5 + - - -
118A GLN* 2.9 35.2 - - - +
119A VAL* 4.0 12.7 - - + +
130A HIS 2.8 16.8 + - - +
131A ARG* 3.4 21.3 + - - +
132A VAL* 2.9 31.5 + - - +
158A LEU* 4.0 2.8 - - + -
159A LEU* 1.3 73.4 - - - +
161A LEU* 1.3 60.7 + - - +
162A PRO* 3.4 2.3 - - - +
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Residues in contact with LEU 161 (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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10A VAL* 4.1 15.3 - - + -
33A ILE* 4.3 10.5 - - + -
98A LEU* 4.3 25.1 - - + -
99A THR 2.8 16.4 + - - +
100A GLY* 3.7 2.8 - - - -
101A SER 3.6 11.9 + - - -
132A VAL* 3.6 27.1 - - + -
138A ILE* 4.2 24.9 - - + -
159A LEU* 4.1 15.5 - - + +
160A ASP* 1.3 76.9 + - - +
162A PRO* 1.3 69.5 - - - +
163A TRP 3.6 0.2 + - - -
165A ILE* 5.1 0.9 - - + -
166A LEU* 3.5 35.5 - - + +
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Residues in contact with PRO 162 (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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101A SER* 3.5 19.7 - - - +
102A GLY 3.5 13.9 - - - +
104A LEU* 3.6 35.4 - - + +
131A ARG* 3.9 6.3 - - + +
132A VAL 3.3 27.4 - - - +
160A ASP* 3.4 8.5 - - - +
161A LEU* 1.3 86.7 - - - +
163A TRP* 1.3 66.4 + - - +
164A ASP* 3.2 0.9 - - + -
165A ILE* 3.0 24.2 + - + +
166A LEU* 3.0 10.9 + - - +
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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