Contacts of the strand formed by residues 195 - 199 (chain A) in PDB entry 3L4U
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 LYS 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASP* 3.4 52.9 - - + +
193A ASN 4.1 2.2 - - - +
194A TRP* 1.3 80.3 - - - +
196A THR* 1.3 71.2 + - - +
197A TRP* 3.6 44.5 - - + +
210A GLY* 5.7 3.0 - - - -
243A VAL 3.7 1.0 - - - +
244A VAL* 3.4 2.8 - - - +
245A LEU* 2.7 40.0 + - + +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP 5.6 0.3 - - - -
195A LYS* 1.3 83.1 + - - +
197A TRP* 1.3 66.8 + - - +
198A PRO* 3.7 7.1 - - - +
210A GLY 5.0 1.4 - - - +
242A GLU* 3.5 43.1 - - + +
243A VAL 3.4 6.1 - - - +
244A VAL* 3.8 19.0 - - + +
254A ARG* 4.9 2.1 + - - +
471A ARG* 3.7 43.0 + - + +
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Residues in contact with TRP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.6 7.6 - - + -
183A HIS* 3.6 39.3 - + + +
184A VAL 3.9 11.9 - - - -
185A HIS* 3.6 36.8 - + + -
190A HIS* 3.8 19.8 - + - -
191A ASP* 5.2 3.3 + - + +
195A LYS* 3.6 42.7 - - + +
196A THR* 1.3 75.5 - - - +
198A PRO* 1.3 68.3 - - - +
199A ILE* 4.1 4.9 - - - +
210A GLY* 3.7 35.7 - - - -
242A GLU* 3.3 2.8 - - - -
243A VAL* 2.9 44.3 + - + +
245A LEU* 3.9 19.7 - - + +
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Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A HIS* 2.7 30.9 + - + -
196A THR 3.7 9.6 - - - +
197A TRP* 1.3 84.8 - - + +
199A ILE* 1.3 54.8 + - - +
210A GLY 4.0 14.6 - - - +
211A THR* 4.3 2.2 - - - -
212A ASN* 3.5 27.2 - - + +
241A MET 3.6 7.9 - - - +
242A GLU* 3.7 4.2 - - + -
471A ARG* 3.4 47.6 - - + +
472A ILE* 4.1 12.6 - - + +
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Residues in contact with ILE 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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180A LEU* 5.0 3.6 - - + -
181A GLY 3.7 18.4 - - - +
182A GLU 5.9 0.2 - - - +
183A HIS* 3.7 13.2 - - - +
197A TRP 4.1 3.1 - - - +
198A PRO* 1.3 79.4 - - - +
200A PHE* 1.3 64.8 + - - +
212A ASN* 4.4 0.7 - - - -
215A GLY 4.5 1.1 - - - +
216A ALA* 3.6 36.6 - - + -
217A GLN 4.0 12.3 - - - +
218A THR* 4.5 9.9 - - + -
240A ALA* 3.8 3.1 - - - -
241A MET* 2.8 51.4 + - + +
243A VAL* 3.8 27.1 - - + -
498A ASN* 4.0 4.7 - - - +
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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