Contacts of the strand formed by residues 111 - 115 (chain A) in PDB entry 3RTC
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A MET* 4.5 0.7 - - - -
35A LEU* 4.0 18.6 - - + -
41A TYR* 3.9 25.4 - - + -
42A ARG 3.0 3.4 + - - +
43A PHE* 3.4 35.4 - - + -
44A LEU* 2.8 32.9 + - - +
109A PHE* 4.5 0.6 - - - +
110A ASP* 1.3 85.7 + - + +
112A VAL* 1.3 68.5 + - - +
113A VAL* 4.4 2.5 - - + -
142A VAL* 3.4 19.5 - - + +
144A VAL* 4.1 18.4 - - + -
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Residues in contact with VAL 112 (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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44A LEU* 3.2 14.8 - - + +
46A LEU* 3.7 31.0 - - + -
106A LEU* 3.8 27.8 - - + -
109A PHE* 5.9 1.8 - - + -
111A VAL* 1.3 75.9 - - - +
113A VAL* 1.3 67.2 + - - +
114A ASP* 3.8 3.7 + - + +
136A VAL* 4.0 18.4 - - + -
141A LYS* 4.1 18.4 - - + -
142A VAL 2.9 10.5 + - - +
143A VAL* 3.5 10.6 - - + +
144A VAL* 2.9 26.9 + - - +
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Residues in contact with VAL 113 (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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27A VAL* 4.9 3.4 - - + -
31A MET* 4.0 31.6 - - + -
43A PHE* 4.2 15.3 - - + -
44A LEU 2.7 9.1 + - - +
45A VAL* 4.0 31.4 - - + -
46A LEU* 2.9 28.9 + - - +
56A GLY* 5.3 0.2 - - - -
59A VAL* 4.2 15.5 - - + -
111A VAL* 4.4 1.3 - - + -
112A VAL* 1.3 75.9 - - - +
114A ASP* 1.3 60.9 + - - +
115A ALA* 3.5 2.5 + - + +
144A VAL* 3.3 6.7 - - + +
146A VAL* 3.8 24.7 - - + -
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Residues in contact with ASP 114 (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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46A LEU* 4.3 7.0 - - + -
112A VAL* 3.8 5.1 + - + -
113A VAL* 1.3 68.7 - - - +
115A ALA* 1.3 57.3 + - - +
116A ILE* 3.3 14.3 + - + +
136A VAL* 6.4 0.2 - - + -
143A VAL* 4.5 4.7 - - + -
144A VAL 2.7 12.0 + - - +
145A SER* 2.7 28.1 + - - +
146A VAL* 2.9 25.9 + - - -
149A PRO* 3.6 0.2 - - - +
150A SER* 2.5 43.7 + - - -
164A VAL* 3.7 21.3 - - + +
491A K 2.9 5.9 - - - -
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Residues in contact with ALA 115 (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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45A VAL* 5.0 0.4 - - + -
46A LEU 2.8 19.4 + - - +
47A CYS* 4.5 0.4 - - - -
48A GLY 3.1 15.1 + - - -
52A ASN* 3.0 32.3 - - - +
53A GLY* 3.2 12.1 - - - -
56A GLY* 3.6 23.8 - - - +
113A VAL* 3.5 3.9 + - + +
114A ASP* 1.3 73.9 - - - +
116A ILE* 1.3 57.7 + - - +
146A VAL* 4.0 10.3 - - + -
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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