Contacts of the strand formed by residues 194 - 202 (chain A) in PDB entry 3KMU
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 ASN 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN 3.6 2.6 + - - +
193A LEU* 1.3 71.7 - - - +
195A PHE* 1.3 64.5 + - - +
196A LEU* 3.1 25.4 - - - +
210A GLY* 3.0 6.1 - - - -
211A ARG* 2.8 59.5 + - + +
217A ILE* 5.5 0.3 - - - +
219A VAL* 6.1 0.2 - - - -
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Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.8 39.7 - + - -
193A LEU* 3.6 29.8 + - + -
194A ASN* 1.3 77.4 + - - +
196A LEU* 1.3 63.8 + - - +
208A TRP* 3.5 54.1 - + + -
209A LYS 4.2 2.0 - - - -
210A GLY* 4.5 1.1 - - - -
219A VAL* 3.8 33.2 - - + -
221A VAL* 4.5 5.8 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASN* 3.1 52.9 - - - +
195A PHE* 1.3 75.0 - - - +
197A THR* 1.3 67.7 + - + +
208A TRP* 4.9 2.0 - - - -
209A LYS* 2.8 37.9 + - - +
210A GLY* 3.8 7.9 - - - -
211A ARG* 3.8 26.5 - - + -
216A ASP* 5.5 0.4 - - - +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PHE 3.9 0.4 - - - -
196A LEU* 1.3 84.6 - - + +
198A LYS* 1.3 67.4 + - - +
199A LEU* 3.6 7.9 + - + +
208A TRP* 3.4 9.2 - - - -
209A LYS* 2.7 58.6 + - + +
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A THR* 1.3 80.1 + - - +
199A LEU* 1.3 65.6 + - - +
200A ASN 3.9 9.9 - - - +
201A GLU* 2.6 32.8 + - + +
206A GLU* 2.8 47.5 + - - -
207A LEU 3.9 8.3 - - - +
208A TRP* 3.5 34.1 - - + +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A THR* 4.4 8.5 - - + +
198A LYS* 1.3 77.2 - - - +
200A ASN* 1.3 63.3 + - + +
207A LEU* 2.7 31.7 + - + +
208A TRP 3.9 5.8 - - - -
209A LYS* 3.6 34.1 - - + +
218A VAL* 4.0 9.9 - - + -
271A TRP* 3.4 35.2 - - + -
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Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 3.8 6.8 - - - +
199A LEU* 1.3 81.6 - - + +
201A GLU* 1.3 67.5 + - - +
202A ASN* 3.8 26.1 - - - +
205A GLY 5.1 0.3 - - - +
206A GLU* 3.3 8.7 - - - +
207A LEU* 2.9 55.0 + - + +
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Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 2.6 38.2 + - + +
200A ASN* 1.3 80.9 + - - +
202A ASN* 1.3 66.1 + - - +
205A GLY 3.4 10.8 - - - +
206A GLU* 4.2 3.9 - - + +
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASN* 3.8 17.5 - - - +
201A GLU* 1.3 77.9 - - - +
203A HIS* 1.3 86.1 + - - +
204A SER* 3.0 25.1 + - - -
205A GLY* 2.9 23.3 + - - +
223A LYS* 5.5 0.9 - - - +
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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