Contacts of the strand formed by residues 194 - 199 (chain F) in PDB entry 1XWD
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 GLN 194 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169F SER 5.5 0.2 + - - -
170F PHE 3.3 25.7 + - - -
171F GLU* 3.9 21.9 + - - +
172F SER* 3.6 8.9 + - - -
173F VAL* 3.0 28.3 + - - +
193F THR* 1.3 73.6 + - - +
195F LEU* 1.3 63.2 + - - +
196F ASP* 3.4 0.6 + - - -
218F SER* 4.0 22.3 + - - +
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Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F VAL* 4.2 5.8 - - + -
175F LEU* 3.4 35.0 - - + -
190F PHE* 3.7 33.9 - - + -
193F THR* 3.5 18.1 + - + -
194F GLN* 1.3 70.7 - - - +
196F ASP* 1.3 63.6 + - - +
197F GLU 4.3 11.0 - - - +
198F LEU* 4.5 4.3 - - + -
214F PHE* 4.2 6.3 - - + -
217F ALA* 4.4 4.3 - - + -
218F SER* 4.2 7.4 - - - +
219F GLY 3.0 32.1 - - - +
220F PRO* 3.8 26.9 - - + -
221F VAL* 3.8 6.6 + - - +
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Residues in contact with ASP 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PRO* 3.7 35.4 - - - +
146F LYS* 5.0 3.3 + - - +
172F SER* 3.0 31.3 + - - +
173F VAL 3.0 16.8 + - - +
174F ILE* 3.8 18.3 - - + +
194F GLN 3.4 1.5 + - - +
195F LEU* 1.3 75.9 - - - +
197F GLU* 1.3 62.7 + - + +
221F VAL* 3.3 27.9 + - - +
222F ILE* 3.3 12.4 + - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D TYR* 6.1 0.2 - - - -
45E PRO* 5.0 10.4 - - - +
173F VAL 3.9 2.4 + - - +
174F ILE* 3.8 29.0 - - + +
175F LEU* 3.0 24.7 + - - +
176F TRP* 3.0 34.7 + - - +
195F LEU* 3.5 5.9 - - - +
196F ASP* 1.3 81.5 + - + +
198F LEU* 1.3 68.4 + - - +
199F ASN* 4.8 6.3 + - + -
220F PRO* 4.9 0.9 - - - -
221F VAL 5.0 0.2 - - - +
222F ILE* 3.3 40.5 - - + +
224F ASP* 6.1 0.7 - - + +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F LEU* 3.4 17.5 - - + +
177F LEU* 4.5 4.3 - - + -
190F PHE* 3.6 42.0 - - + -
195F LEU* 4.5 6.3 - - + -
197F GLU* 1.3 78.2 - - - +
199F ASN* 1.3 69.7 + - - +
200F LEU* 3.6 39.0 - - + -
214F PHE* 4.0 13.2 - - + -
220F PRO* 4.3 8.5 - - + +
222F ILE 2.9 8.4 + - - +
223F LEU* 3.6 21.5 - - + +
224F ASP* 3.0 26.0 + - - +
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Residues in contact with ASN 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU 2.8 9.5 + - - -
176F TRP* 3.4 33.1 - - + +
177F LEU* 2.9 25.2 + - - -
178F ASN* 3.0 18.3 + - + +
197F GLU* 4.8 5.3 + - - +
198F LEU* 1.3 76.1 - - - +
200F LEU* 1.3 59.0 + - - +
201F SER* 2.8 32.9 + - - -
224F ASP* 3.4 25.3 + - + +
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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