Contacts of the strand formed by residues 130 - 136 (chain A) in PDB entry 3NNJ
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PHE* 3.8 15.5 - - - -
124A THR* 5.7 0.2 - - - -
128A ASP 3.6 2.4 + - - -
129A PHE* 1.3 78.3 - - - +
131A ALA* 1.3 64.1 + - - +
223A ASN* 3.3 7.1 - - - +
224A LYS* 2.8 37.7 + - - +
225A TYR* 6.2 0.2 - - - -
248A LEU 3.6 9.9 - - - -
249A VAL* 4.7 0.2 - - - -
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Residues in contact with ALA 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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121A PHE* 3.4 8.3 - - - -
129A PHE* 3.5 24.7 - - + -
130A GLY* 1.3 74.9 - - - +
132A SER* 1.3 68.4 + - - +
221A PHE* 3.8 18.8 - - + -
222A PHE 3.3 13.0 - - - +
223A ASN* 3.6 4.7 - - - +
224A LYS 4.2 0.9 - - - +
248A LEU* 2.9 37.8 + - + +
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Residues in contact with SER 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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121A PHE* 3.6 18.4 - - - -
131A ALA* 1.3 80.7 + - - +
133A ILE* 1.3 64.9 - - - +
134A TRP 4.2 0.4 - - - -
220A PHE 3.6 0.9 - - - +
221A PHE* 3.3 7.1 - - - -
222A PHE* 2.8 61.4 + - - -
245A VAL* 4.3 11.4 - - - +
246A ILE 3.1 10.0 + - - -
247A ARG* 4.1 6.9 - - - +
248A LEU* 4.8 0.2 - - - -
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Residues in contact with ILE 133 (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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21A ILE* 6.6 0.2 - - + -
24A ILE* 5.6 4.9 - - + -
25A PHE* 5.1 6.5 - - + -
80A ILE* 3.9 26.2 - - + -
83A LYS* 6.4 0.4 - - + -
87A LEU* 3.6 27.1 - - + -
132A SER* 1.3 76.1 - - - +
134A TRP* 1.3 60.0 + - - +
135A ILE* 3.9 16.1 + - + -
219A ALA* 4.1 13.9 - - + -
220A PHE 3.3 9.4 - - - +
221A PHE* 4.0 11.9 - - + -
244A PHE 3.2 5.5 - - - +
245A VAL* 3.3 2.9 - - - -
246A ILE* 2.9 43.2 + - + +
248A LEU* 3.5 23.6 - - + -
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Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A SER 4.2 0.2 - - - -
133A ILE* 1.3 72.1 - - - +
135A ILE* 1.3 60.3 + - - +
136A PRO* 3.6 33.2 - - + -
140A ILE* 4.1 8.5 - - + -
146A GLY 4.6 4.5 - - - -
147A GLY* 3.8 31.4 - - - -
148A MSE 3.6 38.3 - - + +
214A TYR* 3.8 25.4 - + - -
219A ALA* 3.4 4.9 - - - +
220A PHE* 2.8 54.8 + - + +
222A PHE* 4.3 7.6 - - + -
243A ALA* 3.2 31.3 - - + +
244A PHE 3.4 2.2 - - - -
245A VAL* 4.1 19.5 - - + +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A PHE* 4.2 17.0 - - + -
30A ILE* 4.3 24.5 - - + -
76A VAL* 5.2 3.1 - - + -
80A ILE* 3.8 29.6 - - + -
133A ILE* 4.1 13.9 - - + -
134A TRP* 1.3 78.2 - - - +
136A PRO* 1.3 71.9 - - + +
137A LEU* 3.4 9.4 + - + +
218A ASP 4.5 4.5 - - - +
219A ALA* 4.2 4.5 - - + -
243A ALA* 3.2 3.5 - - - -
244A PHE* 2.8 47.3 + - + +
246A ILE* 3.8 18.4 - - + -
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Residues in contact with PRO 136 (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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30A ILE* 4.9 2.3 - - - +
134A TRP* 3.6 40.8 - - + +
135A ILE* 1.3 87.2 - - + +
137A LEU* 1.3 62.1 + - - +
138A ASP 3.2 18.9 + - - +
140A ILE* 4.1 7.6 - - + -
214A TYR* 3.9 20.0 - - + +
215A ASN 5.4 2.2 - - - +
216A LEU* 4.4 13.9 - - + +
217A GLY 5.2 1.0 + - - -
218A ASP 3.2 21.2 - - - +
219A ALA* 4.3 0.4 - - - -
242A ARG 3.7 6.3 - - - +
243A ALA* 4.1 6.3 - - + -
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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