Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 4NWO
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.5 29.4 + - - +
66A ASP* 5.2 0.3 + - - -
67A CYS 2.5 24.8 + - - -
68A CYS 3.6 3.6 - - - -
70A ILE* 4.8 5.6 - - - -
122A GLY 3.7 0.3 - - - +
123A LEU* 3.3 9.6 - - - -
124A ARG* 2.9 38.1 + - - -
125A GLY 3.4 1.6 + - - -
126A ASP* 1.3 88.9 + - - +
128A LEU* 1.3 59.7 + - - +
129A ILE* 3.8 3.0 + - - +
157A MET* 4.4 0.4 - - - +
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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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68A CYS 3.0 14.5 + - - +
69A LEU* 3.4 16.3 - - + +
70A ILE 2.8 31.0 + - - -
96A MET* 4.5 9.6 - - + -
99A PHE* 4.1 17.0 - - + -
121A ALA* 4.6 0.7 - - + -
122A GLY 3.6 18.2 - - - +
123A LEU* 3.7 18.6 - - + -
126A ASP 4.3 0.4 + - - -
127A SER* 1.3 72.7 - - - +
129A ILE* 1.3 61.3 + - - +
130A VAL* 4.0 13.7 - - + -
150A ILE* 4.1 31.0 - - + +
153A CYS* 4.0 22.4 - - + -
154A ILE* 5.2 4.9 - - + -
157A MET* 5.0 3.3 - - - -
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Residues in contact with ILE 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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58A LEU* 3.8 32.5 - - + +
62A ALA* 5.2 1.3 - - + -
70A ILE* 3.3 27.8 - - + +
72A THR* 4.3 9.6 - - + -
88A THR* 4.0 20.1 - - + +
91A VAL* 4.1 18.2 - - + -
92A CYS* 3.9 20.0 - - - -
120A THR 4.3 0.2 - - - +
121A ALA* 3.2 8.1 - - - +
122A GLY 2.9 33.2 + - - +
124A ARG* 4.5 13.0 - - + -
127A SER* 4.5 4.9 - - - +
128A LEU* 1.3 76.1 - - - +
130A VAL* 1.3 63.7 + - - +
131A ASN* 4.6 1.3 - - - +
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Residues in contact with VAL 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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69A LEU* 4.4 9.6 - - + -
70A ILE 2.9 11.7 + - - +
71A VAL* 3.6 9.5 - - + +
72A THR* 2.9 25.8 + - - +
99A PHE* 3.9 37.0 - - + -
103A MET* 4.6 7.2 - - + -
120A THR 4.1 2.2 - - - -
121A ALA* 4.0 4.5 - - + -
128A LEU* 4.0 17.7 - - + -
129A ILE* 1.3 80.9 - - - +
131A ASN* 1.3 76.3 + - - +
132A LEU* 3.8 13.6 + - + -
143A LEU* 5.8 1.8 - - + -
146A VAL* 4.7 8.1 - - + -
150A ILE* 4.6 4.7 - - + -
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Residues in contact with ASN 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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72A THR* 2.7 27.2 + - - +
76A THR* 4.1 8.3 - - + -
84A THR* 3.6 7.6 - - - +
85A PRO* 3.5 22.0 - - - +
88A THR* 3.2 30.1 + - - +
103A MET* 3.7 10.9 - - - +
119A GLN* 3.5 26.1 - - + +
120A THR* 3.2 36.1 + - - +
129A ILE* 4.6 0.3 - - - +
130A VAL* 1.3 73.7 - - - +
132A LEU* 1.3 69.3 + - - +
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Residues in contact with LEU 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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28A ILE* 3.9 13.2 - - + -
71A VAL* 3.6 25.1 - - + -
72A THR 2.8 18.3 + - - +
73A THR* 3.3 2.2 - - - -
74A GLY 3.1 16.6 + - - +
76A THR* 3.8 9.0 - - - +
103A MET* 4.1 8.7 - - - -
119A GLN* 4.3 2.0 - - - -
130A VAL* 4.2 11.0 - - + -
131A ASN* 1.3 81.0 - - - +
133A PRO* 1.3 76.3 - - + +
139A ILE* 4.1 20.4 - - + +
142A CYS* 3.9 22.7 - - + +
143A LEU* 3.7 29.2 - - + +
146A VAL* 5.4 0.9 - - + -
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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