Contacts of the strand formed by residues 126 - 132 (chain A) in PDB entry 3C3P
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.0 9.4 - - + +
60A VAL* 3.6 34.5 - - + -
123A GLN* 3.9 17.3 - - + -
124A ARG 4.5 0.7 - - - -
125A ASP* 1.3 75.0 - - - +
127A ASP* 1.3 58.7 + - - +
128A ILE 3.2 32.1 - - - +
129A LEU* 4.0 11.0 - - + +
145A MSE 3.4 33.2 - - + -
148A CYS* 2.9 23.9 + - + +
149A LEU* 3.7 8.2 - - + -
150A ALA* 2.9 22.3 + - - +
153A ALA* 3.2 12.6 - - - +
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Residues in contact with ASP 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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54A LYS* 3.5 17.3 + - - +
56A PRO* 3.5 19.7 - - + -
57A GLN* 2.8 38.6 + - - +
58A LEU 2.9 19.4 + - - +
125A ASP 3.5 6.5 + - - +
126A ILE* 1.3 73.5 - - - +
128A ILE* 1.3 65.4 + - - +
150A ALA* 3.5 18.5 - - - +
151A LYS 4.9 1.7 - - - +
153A ALA* 3.4 6.5 - - - +
154A LEU 2.9 25.3 + - - -
212A EDO 4.7 0.5 + - - -
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Residues in contact with ILE 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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51A ALA* 4.0 26.5 - - + +
54A LYS* 4.1 14.1 - - + -
56A PRO* 4.0 26.7 - - + -
58A LEU 3.1 4.0 + - - -
59A VAL* 3.4 15.8 - - + -
60A VAL 2.9 27.4 + - - +
73A PHE* 4.2 17.5 - - + -
126A ILE* 3.2 6.2 - - - +
127A ASP* 1.3 83.5 - - - +
129A LEU* 1.3 69.1 + - - +
130A PHE 4.5 0.2 - - - +
154A LEU* 3.3 15.9 - - + +
156A ILE* 3.9 25.4 - - + -
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Residues in contact with LEU 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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60A VAL* 3.6 28.5 - - + +
62A PRO* 3.9 21.5 - - + -
126A ILE* 4.0 2.9 - - + +
127A ASP 4.3 0.4 - - - -
128A ILE* 1.3 74.1 - - - +
130A PHE* 1.3 64.1 + - - +
131A MSE 4.4 1.1 - - + -
141A VAL* 4.3 12.6 - - + -
142A LEU* 5.5 3.6 - - + -
145A MSE 3.9 40.2 - - + -
149A LEU* 4.1 23.7 - - + +
154A LEU 3.1 7.8 + - - +
155A LEU* 3.5 28.2 - - + +
156A ILE 3.0 25.3 + - - +
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Residues in contact with PHE 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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39A VAL* 4.1 8.7 - - + -
47A LEU* 3.8 21.8 - - + -
60A VAL 2.9 15.3 + - - +
61A VAL* 3.8 22.0 - - + -
62A PRO* 3.0 29.3 - - + +
63A GLY 4.7 8.3 - - - -
64A ASP* 5.2 1.1 - - - -
69A ALA* 3.8 16.8 - - + -
73A PHE* 3.6 34.8 - + + -
128A ILE* 4.0 1.8 - - + +
129A LEU* 1.3 73.1 - - - +
131A MSE 1.3 76.5 + - - +
132A ASP* 4.6 5.4 - - + -
156A ILE* 3.4 11.0 - - + -
158A VAL* 3.6 42.2 - - + -
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Residues in contact with MSE 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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62A PRO* 5.4 4.5 - - + -
129A LEU* 4.4 1.8 - - + -
130A PHE* 1.3 86.0 - - - +
132A ASP* 1.3 57.7 + - - +
133A CYS* 4.0 3.4 - - - -
136A PHE* 4.8 11.7 - - + +
138A GLY* 4.1 17.3 - - - +
141A VAL* 4.1 33.4 - - + -
142A LEU* 5.5 2.0 - - + -
155A LEU* 2.5 55.6 - - + -
156A ILE 2.7 13.2 + - - +
157A ALA* 3.1 6.4 - - + -
158A VAL* 2.7 35.5 + - - +
181A PHE* 3.9 21.1 - - + -
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Residues in contact with ASP 132 (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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37A PRO* 5.9 4.3 - - - +
62A PRO 5.6 0.6 + - - +
63A GLY 5.8 2.9 - - - +
130A PHE* 4.6 7.1 - - + -
131A MSE 1.3 75.3 - - - +
133A CYS* 1.3 65.2 + - - +
134A ASP* 2.9 17.9 + - - +
135A VAL* 3.1 31.0 + - + +
136A PHE* 3.1 24.0 + - + +
158A VAL* 3.9 10.3 - - + -
159A ASN* 2.7 32.6 + - - -
215A EDO 6.0 1.1 - - - -
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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