Contacts of the strand formed by residues 111 - 115 (chain O) in PDB entry 4V1N
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 THR 111 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105O ARG* 3.7 7.4 - - - +
106O ILE* 3.3 20.1 + - - +
109O PRO* 3.0 16.0 + - + +
110O LYS* 1.3 82.2 - - - +
112O THR* 1.3 66.5 + - - +
123O VAL* 4.4 7.2 - - + -
124O THR 3.5 15.5 - - - +
125O GLY* 4.8 2.2 - - - -
126O ALA* 3.9 24.5 - - + +
132O SER* 5.6 0.2 - - - -
135O ALA* 3.5 19.1 - - + +
139O TYR* 2.9 31.1 + - - -
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Residues in contact with THR 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O ILE* 3.7 28.7 - - + -
104O MET 3.5 6.7 - - - +
105O ARG* 3.2 27.2 + - - +
111O THR* 1.3 74.8 - - - +
113O ALA* 1.3 65.7 + - - +
114O LEU* 4.8 1.6 - - + -
123O VAL* 3.6 2.3 - - - +
124O THR* 2.9 40.5 + - + +
125O GLY* 5.2 0.2 - - - -
139O TYR* 3.5 3.4 - - - -
46T T 4.2 15.0 - - - -
47T A 3.7 21.1 + - - +
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Residues in contact with ALA 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O VAL 3.4 2.6 - - - +
103O ILE* 3.4 4.2 - - - -
104O MET 2.8 31.3 + - - +
112O THR* 1.3 76.5 - - - +
114O LEU* 1.3 65.1 + - - +
115O ILE* 3.8 15.5 - - + -
121O MET* 4.3 6.5 - - + -
122O VAL 3.2 9.4 - - - +
123O VAL* 4.4 1.3 - - + -
139O TYR* 3.7 38.8 + - + -
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Residues in contact with LEU 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N A 3.7 14.4 - - + +
99O PHE* 4.4 9.2 - - + -
101O ALA* 4.4 2.7 - - + -
102O VAL 3.5 2.9 - - - -
103O ILE* 4.0 22.2 - - + -
112O THR* 4.8 2.5 - - + -
113O ALA* 1.3 74.6 - - - +
115O ILE* 1.3 60.8 + - - +
116O PHE* 3.6 18.9 - - + -
121O MET* 3.3 5.5 - - - +
122O VAL* 2.8 44.5 + - + +
124O THR* 5.5 2.7 - - + -
45T T 3.5 24.5 - - - +
46T T 3.6 50.3 - - + +
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Residues in contact with ILE 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O LEU* 4.6 8.1 - - + -
80O LEU* 3.4 32.5 - - + -
82O LEU* 3.6 11.5 - - + +
85O VAL* 4.9 2.5 - - + -
101O ALA* 3.2 5.0 - - - +
102O VAL* 2.9 44.3 + - + +
104O MET* 3.5 46.2 - - + -
113O ALA* 4.2 7.6 - - + -
114O LEU* 1.3 76.3 - - - +
116O PHE* 1.3 61.8 + - - +
120O LYS 4.0 3.4 - - - +
121O MET* 4.0 24.7 - - + -
139O TYR* 4.9 2.0 - - + -
143O ILE* 4.0 12.3 - - + -
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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