Contacts of the strand formed by residues 193 - 196 (chain B) in PDB entry 4GDY
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 PHE 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.9 22.7 - + - -
128B ILE* 3.9 23.3 - - + -
129B ILE* 3.8 21.8 - - + -
134B ASN 4.6 0.6 + - - -
135B VAL* 3.6 35.3 - - + -
136B LEU* 3.0 28.4 + - - +
137B LEU* 6.0 0.2 - - + -
149B LEU* 4.4 7.9 - - + -
191B PRO* 3.5 2.0 - - - +
192B LYS* 1.3 77.8 - - - +
194B LEU* 1.3 69.5 + - - +
195B TYR* 3.7 21.3 - - + -
225B PHE* 4.1 7.4 - - - -
226B LEU* 3.3 25.1 - - + +
228B ILE* 3.6 27.8 - - + -
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.3 20.4 - - + +
137B LEU* 5.1 0.7 - - - +
159B VAL* 4.7 5.2 - - + -
166B ILE* 4.2 19.7 - - + -
171B LEU* 3.8 34.3 - - + -
193B PHE* 1.3 74.6 - - - +
195B TYR* 1.3 58.3 + - - +
196B THR* 4.0 24.5 - - + -
216B ILE* 4.0 21.1 - - + -
225B PHE* 3.8 18.2 - - + -
226B LEU 3.0 6.5 + - - +
227B ILE* 3.5 12.0 - - + +
228B ILE 2.8 30.0 + - - +
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.0 11.2 - - + -
125B PHE* 4.0 12.1 - + + -
136B LEU 2.9 15.0 + - - +
137B LEU* 3.7 29.3 - - + -
138B ASP* 3.5 12.9 - - - +
141B ALA* 5.2 8.3 - - + -
142B TYR* 4.3 2.6 - - - +
145B THR* 3.0 35.8 - - + +
149B LEU* 5.9 0.2 - - + -
193B PHE* 3.7 21.9 - - + -
194B LEU* 1.3 74.9 - - - +
196B THR* 1.3 66.9 + - - +
197B VAL* 3.5 18.8 - - + +
228B ILE* 3.7 20.2 - - + -
230B ASP* 2.6 44.1 + - + -
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Residues in contact with THR 196 (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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138B ASP* 3.9 7.8 + - - -
166B ILE* 3.5 24.9 - - + +
194B LEU* 4.0 17.3 - - + -
195B TYR* 1.3 82.4 - - - +
197B VAL* 1.3 70.1 + - - +
198B PRO* 3.3 12.5 - - + +
208B LEU* 4.1 9.4 - - + +
227B ILE* 4.6 3.1 - - + -
228B ILE 3.1 14.7 + - - +
229B GLU* 3.8 0.4 - - - -
230B ASP 3.1 23.2 + - - -
246B PHE* 4.0 26.0 - - + -
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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