Contacts of the strand formed by residues 116 - 120 (chain B) in PDB entry 5V6Y
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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114B ALA 3.7 1.2 + - - -
115B LEU* 1.3 74.8 + - - +
117B LEU* 1.3 63.0 + - - +
118B ILE* 3.7 5.7 + - - +
228B ILE* 3.8 4.2 - - - +
229B ASN 3.3 26.4 + - - +
234B TRP* 5.7 2.2 - - - -
246B VAL* 3.7 23.6 - - - -
247B THR 3.8 1.6 - - - -
249B LEU* 3.5 12.6 - - - +
322B THR* 3.4 29.6 + - - -
325B ASN* 3.2 20.8 + - - +
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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
----------------------------------------------------------
116B SER* 1.3 73.7 - - - +
118B ILE* 1.3 69.4 + - - +
119B TYR* 4.1 0.8 + - + -
127B PRO* 4.2 10.5 - - + -
128B PRO 4.0 17.3 - - - +
149B LEU* 5.0 3.1 - - + -
226B MET* 4.2 25.6 - - + -
227B THR 4.1 9.4 - - - +
228B ILE* 4.5 10.3 - - + -
245B GLY 3.5 3.3 - - - +
247B THR* 3.0 43.5 + - + +
248B VAL 3.3 28.7 - - - +
249B LEU* 3.6 8.3 - - + +
250B PRO* 3.7 25.1 - - + -
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Residues in contact with ILE 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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116B SER* 4.5 8.1 - - - +
117B LEU* 1.3 78.6 - - - +
119B TYR* 1.3 62.6 + - - +
219B PHE* 3.4 30.4 - - + -
226B MET* 3.3 5.2 - - - +
227B THR* 2.9 47.1 + - + +
229B ASN* 5.0 12.8 - - + +
234B TRP* 4.1 16.8 - - + +
237B ILE* 4.2 10.1 - - + -
244B TYR* 4.1 13.5 - - + -
245B GLY 3.3 16.4 - - - +
246B VAL* 3.5 30.7 - - + -
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Residues in contact with TYR 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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117B LEU* 5.0 1.3 - - + -
118B ILE* 1.3 75.8 - - - +
120B ASN* 1.3 60.4 + - - +
121B LYS* 3.5 33.2 - - + +
124B LEU* 3.3 29.8 - - + -
125B PRO 4.0 9.5 + - - -
127B PRO* 3.4 38.9 - - + +
219B PHE* 3.5 8.1 - - - -
225B ALA 3.3 10.5 - - - +
226B MET* 3.8 13.5 - - + -
244B TYR* 3.3 7.6 - - - -
245B GLY* 3.2 49.6 + - - -
246B VAL 4.2 1.1 - - - -
247B THR* 4.1 19.3 - - + -
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Residues in contact with ASN 120 (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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119B TYR* 1.3 72.0 - - - +
121B LYS* 1.3 59.7 + - - +
122B ASP* 2.9 37.8 + - - +
123B LEU* 3.7 28.8 - - + +
124B LEU* 2.8 32.7 + - - +
219B PHE* 4.2 9.0 + - + -
222B GLY* 4.3 16.0 - - - -
224B THR 4.6 2.8 + - - -
225B ALA* 2.8 21.4 + - - +
242B VAL* 3.6 20.9 - - - +
243B ASN 3.6 9.0 + - - +
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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