Contacts of the strand formed by residues 83 - 87 (chain A) in PDB entry 4YVG
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 LYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLY 3.8 2.2 + - - -
82A ALA* 1.3 71.9 - - - +
84A VAL* 1.3 61.1 + - - +
85A ILE* 3.9 15.2 + - + -
101A GLU* 5.4 4.8 + - - +
102A LEU* 5.2 1.5 - - + +
105A ASN* 3.9 30.8 + - - +
107A LYS 3.5 5.5 + - - -
108A LEU* 3.4 18.3 - - + +
109A ILE 2.9 23.7 + - - +
128A ASP* 3.5 19.1 - - + -
129A GLU* 2.9 38.9 + - - +
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Residues in contact with VAL 84 (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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71A ILE* 4.9 6.3 - - + -
75A LYS* 4.1 22.0 - - + +
82A ALA 4.0 7.6 - - - +
83A LYS* 1.3 74.3 - - - +
85A ILE* 1.4 64.1 + - - +
109A ILE* 3.4 28.5 - - + +
111A VAL* 3.9 15.3 - - + -
126A GLU 3.5 25.6 - - - +
127A ILE* 3.8 16.9 - - + +
128A ASP* 2.8 44.0 + - - +
129A GLU 3.2 7.8 + - - +
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Residues in contact with ILE 85 (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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83A LYS* 4.2 15.3 - - + +
84A VAL* 1.4 78.0 - - - +
86A TYR* 1.3 71.0 + - - +
87A LEU* 4.1 6.6 + - + +
102A LEU* 3.6 31.9 - - + -
108A LEU* 4.2 12.3 - - + -
109A ILE 2.8 7.8 + - - +
110A LEU* 3.6 27.0 - - + -
111A VAL* 2.8 28.6 + - - +
127A ILE* 4.3 2.5 - - - -
129A GLU* 3.1 6.7 - - + +
131A TRP* 3.6 34.8 - - + +
148A LEU* 4.5 7.6 - - + -
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Residues in contact with TYR 86 (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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85A ILE* 1.3 74.6 - - - +
87A LEU* 1.3 72.1 + - - +
88A SER* 3.4 20.0 + - - -
90A GLN* 5.9 0.4 - - - -
111A VAL* 3.3 20.6 - - + -
113A GLY 4.0 9.4 - - - -
117A GLY* 3.6 3.5 - - - -
118A ILE* 3.6 46.3 + - + -
123A ILE* 3.8 25.1 - - + -
127A ILE* 3.6 27.6 - - + +
129A GLU 3.0 6.5 + - - -
130A GLU* 3.3 24.2 - - + +
131A TRP 3.0 23.7 + - - -
301A SAM 2.7 29.5 + - - -
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Residues in contact with LEU 87 (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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85A ILE* 4.4 7.0 - - + -
86A TYR* 1.3 80.7 - - - +
88A SER* 1.3 56.0 + - - +
110A LEU* 4.1 18.8 - - + -
111A VAL 3.3 20.9 + - - +
113A GLY 5.0 0.5 + - - -
131A TRP* 3.3 17.0 - - + +
133A ILE* 5.0 4.3 - - + -
141A GLY* 3.8 13.0 - - - +
144A PRO* 3.9 23.1 - - + +
145A ALA* 3.8 31.0 - - + +
148A LEU* 4.2 19.1 - - + -
301A SAM 2.7 37.8 + - + +
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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