Contacts of the strand formed by residues 214 - 219 (chain B) in PDB entry 3KAS
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 TYR 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ASN* 5.8 0.2 - - - -
111B ARG 3.9 0.2 - - - +
112B VAL* 3.2 7.6 - - - +
113B SER* 2.6 38.4 + - - +
114B ASP 3.9 3.6 - - - -
115B ILE 3.5 26.2 - - - +
116B SER* 3.4 24.0 + - - -
176B GLN* 4.0 18.2 - - + -
177B PHE 3.2 15.0 - - - +
178B ASN* 3.5 24.7 - - + -
179B ILE* 4.1 6.7 - - - -
212B VAL* 2.8 41.3 - - + +
213B CYS* 1.3 79.1 - - - +
215B LEU* 1.3 60.3 + - - +
216B THR* 4.3 9.9 + - - +
1D NAG 2.7 33.1 + - + +
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Residues in contact with LEU 215 (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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110B ILE* 3.9 12.1 - - + -
111B ARG 3.4 7.6 - - - +
112B VAL* 4.2 7.4 - - + +
148B PHE* 4.5 3.4 - - + -
152B LEU* 4.0 7.0 - - + -
175B ILE 3.6 0.5 - - - +
176B GLN* 3.4 4.0 - - - +
177B PHE* 2.7 63.7 + - + -
179B ILE* 4.1 12.4 - - + +
192B ILE* 4.0 16.2 - - + -
196B MET* 3.7 40.4 - - + -
214B TYR* 1.3 75.0 - - - +
216B THR* 1.3 63.6 + - - +
217B ILE* 3.8 20.0 - - + -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 4.6 24.3 - - + -
109B LEU 3.5 0.9 - - - +
110B ILE* 3.3 4.5 - - - +
111B ARG* 2.8 41.1 + - - +
113B SER* 5.7 0.3 + - - -
115B ILE 4.4 7.6 + - - -
117B VAL* 5.9 0.9 - - + -
174B ASN* 3.6 25.3 + - - +
175B ILE 3.3 4.8 + - - +
176B GLN* 4.5 8.5 + - - +
214B TYR* 4.3 13.0 + - - +
215B LEU* 1.3 76.7 + - - +
217B ILE* 1.3 66.9 + - - +
218B ASN* 3.6 20.0 - - - +
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Residues in contact with ILE 217 (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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101B MET* 5.3 0.9 - - + -
108B PHE* 3.7 25.4 - - + -
109B LEU 3.2 8.7 - - - +
110B ILE* 4.1 8.7 - - + -
145B ILE* 4.2 28.7 - - + -
148B PHE* 3.8 33.2 - - + -
174B ASN* 3.3 7.4 + - - -
175B ILE* 2.9 43.8 + - + +
177B PHE* 3.9 17.5 - - + -
215B LEU* 3.8 11.7 - - + -
216B THR* 1.3 79.4 - - - +
218B ASN* 1.3 65.6 + - - +
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Residues in contact with ASN 218 (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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108B PHE* 3.4 3.6 - - - -
109B LEU* 2.7 43.2 + - + +
111B ARG* 3.0 28.5 + - - +
173B SER* 2.9 24.0 + - - -
174B ASN* 3.2 22.4 + - - -
216B THR* 3.6 9.6 - - - +
217B ILE* 1.3 78.3 + - - +
219B GLN* 1.3 63.7 + - - +
224B SER* 3.2 36.0 + - - +
225B SER* 4.2 8.1 - - - -
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Residues in contact with GLN 219 (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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106B ASN* 3.2 32.5 + - + +
107B THR 3.6 13.7 - - - +
108B PHE* 3.8 24.2 - - + -
136B LEU* 3.8 21.7 - - + +
137B ASN* 4.6 9.4 + - - +
138B LYS* 5.4 1.9 + - - +
141B SER* 4.0 8.3 + - - -
173B SER* 2.9 20.4 + - - +
175B ILE* 6.2 0.4 - - - +
217B ILE 4.3 0.2 - - - -
218B ASN* 1.3 71.7 - - - +
220B CYS* 1.3 70.5 + - - +
222B ASP* 3.1 26.5 + - - +
225B SER* 3.7 4.8 - - - -
1011B NAG 3.4 26.7 + - + +
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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