Contacts of the strand formed by residues 192 - 200 (chain A) in PDB entry 4FYT
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 GLY 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ALA* 1.3 74.5 - - - +
193A PHE* 1.3 58.3 + - - -
194A TYR* 3.5 1.9 - - - -
210A THR* 3.0 7.3 - - - -
211A GLN 2.8 42.1 + - - -
212A MET* 4.1 8.5 - - - -
216A ASP* 3.6 25.1 - - - +
219A LYS* 4.3 8.7 - - - -
220A SER* 5.1 0.2 - - - -
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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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89A LEU* 4.1 26.7 - - + -
91A PRO* 3.9 27.4 - - + -
103A PHE* 3.7 39.6 - + + -
185A GLU 3.9 14.6 - - - +
186A LEU* 3.7 11.6 - - + +
187A ALA 4.5 0.5 + - - -
191A ALA 3.9 3.3 - - - +
192A GLY* 1.3 69.8 - - - -
194A TYR* 1.3 60.0 + - - +
208A ALA* 3.7 28.9 - - + -
209A THR 3.4 12.1 - - - -
210A THR* 3.6 12.1 - - + -
219A LYS* 4.6 4.8 + - - +
220A SER* 4.0 22.5 - - - +
237A LEU* 5.0 3.6 - - + -
282A PHE* 3.7 30.3 - - + -
284A VAL* 5.2 2.7 - - + -
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Residues in contact with TYR 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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186A LEU* 3.7 9.6 - - - +
187A ALA 3.2 14.4 - - - +
189A ASP* 3.6 14.6 - - - +
190A LEU* 3.5 48.2 - - + -
191A ALA 3.7 2.0 - - - +
192A GLY 3.5 12.3 - - - -
193A PHE* 1.3 73.5 - - - +
195A ARG* 1.3 83.0 + - - +
196A SER* 4.5 0.9 - - - -
208A ALA* 3.5 4.0 - - - -
209A THR* 2.8 54.9 + - + +
210A THR 3.7 22.4 + - - -
211A GLN* 3.8 2.2 - - + +
348A ASP 2.7 30.1 + - - -
349A PHE* 3.5 22.2 - - - -
350A ASN 4.8 0.2 + - - -
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Residues in contact with ARG 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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101A TYR* 3.4 43.3 - - - +
185A GLU* 4.5 7.9 + - - -
186A LEU* 2.9 38.9 + - + +
187A ALA* 2.9 17.5 + - - +
188A ASP* 3.6 44.2 + - + +
190A LEU* 5.1 0.7 - - - +
194A TYR* 1.3 87.7 - - - +
196A SER* 1.3 59.9 + - - +
197A GLU* 2.9 29.0 + - + +
206A VAL* 4.1 10.3 - - + -
207A VAL 3.2 9.4 - - - +
348A ASP* 4.8 3.5 - - - +
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Residues in contact with SER 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 TYR* 4.2 0.4 + - - -
195A ARG* 1.3 73.9 - - - +
197A GLU* 1.3 64.1 + - - +
205A LYS 3.9 0.2 - - - +
206A VAL* 3.5 0.5 - - - +
207A VAL* 2.8 44.1 + - - +
209A THR* 4.3 15.0 - - - +
346A LEU* 4.7 1.6 - - - -
347A PRO* 3.4 16.9 - - - +
348A ASP* 2.7 49.5 + - - -
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Residues in contact with GLU 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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101A TYR* 4.3 9.4 + - - -
188A ASP* 5.5 1.7 - - - +
195A ARG* 2.9 34.8 + - + -
196A SER* 1.3 81.2 + - - +
198A TYR* 1.3 64.1 + - - +
204A ARG* 3.2 38.8 + - - +
205A LYS 3.3 4.5 - - - +
206A VAL* 4.1 19.3 - - + -
347A PRO* 3.8 2.6 - - - +
348A ASP* 2.8 8.7 + - - +
855A ARG* 3.0 27.9 + - - +
1024A SO4 4.4 0.2 + - - -
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Residues in contact with TYR 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 GLU* 1.3 77.0 - - - +
199A MET* 1.3 67.7 + - - +
200A GLU* 4.6 13.4 + - + -
204A ARG* 3.7 10.6 + - - +
205A LYS* 2.8 70.2 + - + +
207A VAL* 3.8 15.3 - - + +
286A GLU* 4.0 13.3 + - - +
287A PHE* 3.8 31.5 - + - -
305A ARG* 3.4 47.8 - - + +
306A PRO* 3.9 12.6 - - - +
347A PRO* 3.9 15.9 - - + -
1024A SO4 3.5 9.0 - - - +
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Residues in contact with MET 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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198A TYR* 1.3 82.2 - - - +
200A GLU* 1.3 60.4 + - - +
201A GLY 3.7 11.7 + - - +
202A ASN* 3.4 42.4 - - - +
203A VAL 3.4 7.0 - - - -
204A ARG* 3.5 47.6 - - + +
305A ARG* 4.0 4.7 + - - -
1024A SO4 2.8 30.4 + - - +
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Residues in contact with GLU 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 TYR* 4.2 7.5 - - + -
199A MET* 1.3 73.5 - - - +
201A GLY* 1.3 62.9 + - - +
202A ASN 3.3 0.5 + - - -
203A VAL* 2.9 27.4 + - - +
205A LYS* 3.5 36.2 + - + +
286A GLU* 4.0 4.8 - - - +
306A PRO* 3.7 33.9 - - - +
307A SER* 4.7 10.6 + - - +
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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