Contacts of the strand formed by residues 108 - 113 (chain B) in PDB entry 1NUA
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.4 9.4 - - + -
34B CYS* 3.8 21.3 - - + +
36B SER* 3.9 4.0 - - - -
38B THR 3.1 4.6 + - - +
39B TYR* 3.3 27.7 - - + +
40B VAL 2.9 21.3 + - - +
106B ASP 3.6 0.9 - - - +
107B THR* 1.3 81.0 - - - +
109B VAL* 1.3 65.2 + - - +
110B ILE* 3.8 13.6 + - + +
133B ARG* 3.4 42.0 - - + +
134B TYR* 4.6 2.0 - - - +
135B VAL* 4.5 8.5 - - + -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.2 12.3 - - + +
42B VAL* 4.0 11.4 - - + -
96B MET* 4.4 14.6 - - + -
107B THR* 4.2 11.0 - - + -
108B VAL* 1.3 74.6 - - - +
110B ILE* 1.3 63.7 + - - +
121B THR* 3.3 32.1 - - + +
124B VAL* 5.9 3.4 - - + -
125B ALA* 3.9 17.5 - - + +
132B VAL* 4.1 11.2 - - + -
133B ARG 3.0 13.2 + - - +
134B TYR* 3.1 11.6 - - + +
135B VAL* 2.9 28.6 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 4.4 9.4 - - + -
26B VAL* 5.6 0.4 - - + -
30B LEU* 3.3 36.8 - - + -
39B TYR* 4.6 6.7 - - + -
40B VAL 2.5 29.2 + - - +
41B LEU* 3.6 27.6 - - + -
42B VAL* 2.7 34.7 + - - +
55B PHE* 5.5 3.1 - - + -
72B LEU* 5.4 3.1 - - + -
108B VAL* 4.2 11.7 - - + +
109B VAL* 1.3 75.9 - - - +
111B ALA* 1.3 61.0 + - - +
121B THR* 3.9 2.5 - - - +
135B VAL* 3.5 16.4 - - + -
137B VAL* 3.8 24.5 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL 4.0 1.8 - - - -
109B VAL 4.0 0.2 + - - -
110B ILE* 1.3 73.5 - - - +
112B LEU* 1.3 59.5 + - - +
113B GLY 3.6 2.6 + - - +
117B ILE* 4.1 1.6 - - - +
118B GLY* 4.4 8.9 - - - +
121B THR* 3.5 31.2 - - + +
134B TYR* 4.8 3.6 - - + -
135B VAL 3.0 19.7 + - - +
136B GLN* 3.6 20.1 - - - +
137B VAL* 3.0 27.7 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 3.4 30.3 - - + -
41B LEU* 3.6 13.7 - - + -
42B VAL 2.8 10.8 + - - +
43B THR* 2.9 56.0 + - + +
47B ILE* 4.3 6.3 - - + +
51B TYR* 4.3 14.8 - - + -
52B THR* 4.7 10.1 - - - +
110B ILE* 3.6 0.8 + - + -
111B ALA* 1.3 70.3 - - - +
113B GLY* 1.3 57.7 + - - +
117B ILE* 3.5 2.7 - - - +
137B VAL* 3.4 34.5 - - + +
139B THR* 4.0 7.2 - - - +
179B PHE* 3.9 18.2 - - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.7 14.1 - - - -
111B ALA 3.6 3.3 + - - +
112B LEU* 1.3 76.0 - - - +
114B GLY* 1.3 63.4 + - - +
117B ILE* 3.7 10.1 - - - +
118B GLY* 4.9 1.1 + - - -
137B VAL 3.4 6.5 + - - +
138B PRO* 3.4 8.5 - - - +
139B THR* 2.9 34.6 + - - -
143B ALA* 4.6 0.2 - - - +
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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