Contacts of the strand formed by residues 114 - 118 (chain B) in PDB entry 5VKE
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A THR* 4.7 11.0 - - - +
112B ALA 3.7 3.2 + - - -
113B PRO* 1.3 69.7 - - - +
115B VAL* 1.3 61.5 + - - +
116B SER* 3.9 12.1 + - - +
135B PHE* 3.4 5.2 - - - +
137B ASN* 2.9 41.7 + - + +
138B ASN* 5.5 3.7 - - - +
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Residues in contact with VAL 115 (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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113B PRO* 3.6 15.8 + - + +
114B THR* 1.3 75.0 - - - +
116B SER* 1.3 68.0 + - - +
134B CYS* 3.8 13.9 - - - -
135B PHE 3.3 3.1 - - - -
136B LEU* 3.6 31.2 - - + -
194B CYS* 4.3 3.8 - - - +
196B ALA* 4.8 1.8 - - + -
205B ILE* 3.6 39.4 - - + +
207B LYS* 3.5 45.9 + - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 3.9 21.7 + - - +
114B THR* 3.9 8.0 + - - +
115B VAL* 1.3 77.4 + - - +
117B ILE* 1.3 61.4 + - - +
118B PHE* 3.6 26.7 - - - -
134B CYS* 3.3 7.7 - - - -
135B PHE* 2.9 35.0 + - - -
207B LYS* 4.6 3.4 - - - -
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Residues in contact with ILE 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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131A PRO* 5.0 1.6 - - - +
132A GLY 4.9 6.1 + - - -
116B SER* 1.3 74.9 - - - +
118B PHE* 1.3 72.6 + - - +
119B PRO* 4.2 3.9 - - - +
132B VAL* 4.1 9.6 - - + -
133B VAL 3.6 7.6 - - - +
134B CYS* 4.4 0.9 - - + +
148B TRP* 4.0 17.9 - - + -
192B TYR 3.7 23.8 - - - +
194B CYS* 4.0 23.6 - - + +
207B LYS* 4.0 24.9 - - + +
208B SER 4.1 16.2 - - - +
209B PHE* 3.8 20.4 - - + +
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Residues in contact with PHE 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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129A LEU* 3.5 42.4 - - + -
130A ALA 3.5 24.5 - - - +
131A PRO* 4.0 6.1 - - + -
142A THR* 3.1 34.3 - - + -
143A LEU* 4.3 3.4 - - - -
116B SER* 3.6 30.7 - - - -
117B ILE* 1.3 81.9 - - - +
119B PRO* 1.3 70.8 - - + +
131B SER 4.3 0.3 - - - +
132B VAL* 3.5 8.3 - - - +
133B VAL* 2.8 42.9 + - + +
135B PHE* 3.6 29.8 - + - -
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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