Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 6ZGI
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 SER 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE 3.5 11.4 + - - -
107B GLY* 4.0 2.6 - - - -
108B THR 4.8 0.3 + - - -
110B LEU* 3.8 26.7 + - - +
114B THR* 4.6 4.0 + - - -
115B GLN* 1.3 76.6 + - - +
117B LEU* 1.3 60.1 + - - +
130B VAL* 3.3 4.8 - - - +
131B CYS 2.9 32.8 + - - +
133B PHE* 3.6 13.3 + - - -
135B PHE* 3.5 26.9 - - - -
233B ILE* 4.2 5.8 - - - -
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Residues in contact with LEU 117 (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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105B ILE* 3.4 6.4 - - - +
106B PHE* 2.9 57.0 + - + +
116B SER* 1.3 74.3 - - - +
118B LEU* 1.3 62.1 + - - +
119B ILE* 4.2 11.7 - - + -
128B ILE* 3.9 23.6 - - + -
129B LYS 3.5 14.6 - - - +
130B VAL* 3.7 19.3 - - + +
133B PHE* 4.9 0.2 - - - -
135B PHE* 5.2 0.7 - - - -
201B PHE* 4.2 21.5 - - + -
229B LEU* 4.7 1.6 - - + -
231B ILE* 3.9 26.5 - - + -
233B ILE* 4.1 12.7 - - + +
235B ILE* 4.6 1.1 - - + -
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Residues in contact with LEU 118 (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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104B TRP 3.9 3.8 - - - +
105B ILE* 3.7 24.2 - - + -
116B SER 4.2 0.2 - - - -
117B LEU* 1.3 73.1 - - - +
119B ILE* 1.3 66.5 + - - +
120B VAL* 4.0 31.2 - - + -
127B VAL* 3.5 4.0 - - + +
128B ILE* 3.3 5.7 - - - +
129B LYS* 2.9 48.3 + - + +
133B PHE* 4.1 20.0 - - + -
135B PHE* 4.7 2.5 - - + -
157B PHE* 5.0 3.8 - - + -
159B VAL* 4.3 8.5 - - + -
160B TYR* 4.2 24.9 - - + -
241B LEU* 4.1 9.6 - - + -
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Residues in contact with ILE 119 (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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103B GLY* 3.3 5.1 - - - -
104B TRP* 2.9 57.5 + - + +
106B PHE* 4.0 22.0 - - + -
117B LEU* 4.2 12.3 - - + -
118B LEU* 1.3 76.8 - - - +
120B VAL* 1.3 63.0 + - - +
126B VAL* 5.2 6.3 - - + -
127B VAL 3.6 2.2 - - - -
128B ILE* 4.1 27.4 - - + -
194B PHE* 5.3 1.3 - - + -
201B PHE* 4.2 8.5 - - + -
203B ILE* 4.1 25.6 - - + -
229B LEU* 4.7 5.4 - - + -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG 4.0 6.7 - - - +
118B LEU* 4.0 23.6 - - + -
119B ILE* 1.3 77.1 - - - +
121B ASN* 1.3 70.1 + - - +
122B ASN* 4.1 5.1 + - + +
126B VAL* 3.6 6.7 - - - +
127B VAL* 2.9 56.4 + - + +
141B LEU* 4.6 10.5 - - + -
157B PHE* 4.2 29.2 - - + -
241B LEU* 4.0 20.6 - - + -
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Residues in contact with ASN 121 (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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102B ARG* 3.2 46.2 + - - +
120B VAL* 1.3 77.6 - - - +
122B ASN* 1.3 84.9 + - - +
125B ASN 3.7 3.1 - - - -
126B VAL* 4.2 16.9 - - + +
141B LEU* 5.5 0.2 - - - +
175B PHE* 3.6 11.7 - - - -
177B MET* 3.4 31.6 - - - +
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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