Contacts of the strand formed by residues 105 - 109 (chain D) in PDB entry 3VZC
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 LEU 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D LEU* 3.4 35.7 - - + +
77D VAL* 5.1 0.7 - - + -
84D MET* 4.1 18.8 - - + -
87D VAL* 4.4 5.4 - - + -
88D VAL* 3.8 22.0 - - + -
91D LEU* 4.0 17.7 - - + -
101D ILE 5.5 0.2 - - - +
103D LYS 3.2 21.7 + - - +
104D PRO* 1.3 78.3 - - - +
106D CYS* 1.3 60.7 + - - +
359D PHE* 3.7 28.5 - - + -
360D TRP 3.0 10.8 + - - +
361D MET* 3.1 11.8 - - + +
362D VAL* 2.9 27.8 + - - +
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Residues in contact with CYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ALA* 5.7 1.6 - - + -
75D LEU 3.0 6.9 + - - +
76D VAL* 3.5 18.3 - - + -
77D VAL* 2.8 31.5 + - - +
84D MET* 3.8 4.5 - - - +
105D LEU* 1.3 77.4 - - - +
107D SER* 1.3 64.3 + - - +
108D LEU* 3.8 16.8 + - - -
138D CYS 4.9 1.1 - - - -
142D LEU* 3.9 27.1 - - + -
361D MET* 5.2 1.6 - - - -
362D VAL* 3.6 35.9 - - + +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 3.7 4.7 + - - +
80D GLY 5.0 8.8 + - - -
81D ASP* 5.2 1.9 + - - -
84D MET* 3.8 18.9 - - - +
106D CYS* 1.3 75.0 - - - +
108D LEU* 1.3 65.6 + - - +
109D PRO* 4.0 1.4 - - - +
116D LEU* 4.3 13.3 - - - +
117D ALA* 4.3 16.8 + - - +
120D LEU* 4.3 22.3 - - - +
138D CYS* 3.7 21.3 - - - +
361D MET* 4.9 1.8 - - - -
362D VAL* 5.5 0.8 + - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 5.4 0.4 - - + -
38D VAL* 3.8 30.3 - - + -
76D VAL* 3.8 23.1 - - + -
77D VAL 2.8 14.7 + - - +
78D MET* 3.3 25.0 - - + -
79D SER 3.2 23.9 + - - +
106D CYS* 3.8 14.8 + - - -
107D SER* 1.3 79.3 + - - +
109D PRO* 1.3 70.3 - - + +
135D LEU* 4.2 2.0 - - + -
138D CYS* 3.7 11.0 - - + +
139D THR* 3.5 37.0 - - - +
142D LEU* 4.4 6.3 - - + -
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Residues in contact with PRO 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 5.7 0.2 - - - +
79D SER 3.7 0.2 - - - +
107D SER* 4.0 2.0 - - - +
108D LEU* 1.3 82.0 - - - +
110D ALA* 1.3 60.5 + - - +
114D ASN* 3.4 36.1 - - + +
117D ALA* 3.9 8.7 - - + -
131D ASN 4.8 3.1 - - - +
134D LEU* 3.8 20.2 - - + +
135D LEU* 3.5 49.4 - - + +
138D CYS* 3.8 19.7 - - + -
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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