Contacts of the strand formed by residues 192 - 197 (chain A) in PDB entry 5FL6
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 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.3 41.1 - - + +
46A ARG 2.6 30.1 + - - -
48A LEU* 3.5 20.5 - - + +
82A LEU 4.3 4.3 + - - -
189A PHE 3.6 20.0 - - - -
190A SER 3.7 12.6 - - - -
191A ARG* 1.3 74.8 - - - +
193A PHE* 1.3 71.7 + - - +
194A GLN* 3.9 19.1 + - + -
211A THR* 3.5 23.8 - - + -
212A VAL 3.3 16.4 - - - +
213A PHE* 4.0 7.6 - + + -
214A ASN 4.0 2.9 - - - +
256A ALA* 3.4 2.1 - - - -
257A SER* 2.9 34.4 + - - -
258A PHE* 3.6 7.3 - - - -
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Residues in contact with PHE 193 (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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34A ILE* 3.8 44.2 - - + -
36A PRO* 4.1 23.8 - - + -
39A ALA* 4.2 14.6 - - + -
109A VAL* 5.4 7.2 - - + -
146A PHE* 6.5 0.4 - + - -
192A TYR* 1.3 78.0 - - - +
194A GLN* 1.3 62.5 + - - +
195A TYR* 5.6 0.9 - - + -
211A THR* 3.3 4.0 - - - -
212A VAL* 2.8 46.8 + - + +
213A PHE 5.1 0.9 - - - -
214A ASN* 4.8 17.0 - - - -
254A ILE* 3.8 11.2 - - + -
255A GLU 3.1 8.3 - - - +
256A ALA* 4.0 18.6 - - + -
258A PHE* 3.7 29.2 - + - -
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Residues in contact with GLN 194 (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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45A LEU* 3.4 26.3 - - + +
48A LEU* 5.1 0.2 - - - +
82A LEU* 4.0 16.4 + - - +
86A ARG* 3.2 21.1 + - - +
192A TYR* 3.9 21.2 + - + -
193A PHE* 1.3 75.4 - - - +
195A TYR* 1.3 63.5 + - - +
209A ILE* 3.8 18.0 - - + +
210A TRP 3.2 15.5 - - - +
211A THR* 2.9 20.6 + - - -
253A VAL 4.6 0.3 - - - +
254A ILE* 4.3 0.7 - - - -
255A GLU* 2.7 46.9 + - + +
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Residues in contact with TYR 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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30A SER* 3.0 31.9 + - - -
31A PRO* 3.8 1.2 - - - +
32A VAL* 3.6 27.4 - - + +
34A ILE* 5.6 2.0 - - + -
107A HIS* 2.7 34.2 + + - -
193A PHE* 5.6 0.7 - - + -
194A GLN* 1.3 81.9 - - - +
196A GLU* 1.3 72.8 + - - +
197A GLY* 4.2 0.2 - - - -
209A ILE* 3.7 5.0 - - - +
210A TRP* 2.8 54.8 + + + +
212A VAL* 4.6 8.1 - - + -
249A LEU* 4.9 4.0 - - + -
252A ARG* 3.8 20.4 - - + -
253A VAL 4.7 4.9 - - - +
254A ILE* 4.1 28.3 - - + -
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Residues in contact with GLU 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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28A PHE* 4.9 0.9 - - - +
137A PRO* 4.6 9.9 - - - +
138A GLY 5.2 1.8 - - - -
195A TYR* 1.3 77.7 - - - +
197A GLY* 1.3 61.3 + - - +
207A GLY* 3.3 29.0 + - - +
208A VAL 3.4 10.8 - - - +
209A ILE* 4.1 19.9 - - + +
252A ARG* 3.0 33.3 + - + +
86B ARG* 3.4 39.4 + - - +
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Residues in contact with GLY 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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28A PHE* 3.4 16.8 - - - -
30A SER* 3.4 12.3 - - - -
195A TYR* 4.0 1.4 + - - -
196A GLU* 1.3 75.1 - - - +
198A SER* 1.3 61.3 + - - -
206A GLN* 3.4 1.4 - - - +
207A GLY 3.1 11.8 + - - -
208A VAL* 2.8 32.9 + - - -
210A TRP* 4.1 1.9 - - - -
252A ARG* 3.5 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