Contacts of the strand formed by residues 192 - 202 (chain A) in PDB entry 4JF7
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 ASN 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.3 7.2 + - - -
180A VAL* 2.7 33.6 + - - +
182A LEU* 4.0 20.8 - - - +
191A SER* 1.3 83.8 - - - +
193A GLN* 1.3 63.2 + - - +
217A TYR* 3.2 34.5 + - + +
218A LEU 3.4 8.5 - - - +
219A SER* 3.3 35.0 + - - +
220A ASP 4.4 0.9 + - - -
221A GLY* 4.7 2.3 + - - -
222A VAL 5.3 0.6 - - - +
224A ARG* 5.7 0.7 - - - -
203B THR* 5.3 2.0 - - - -
204B SER* 4.2 7.9 + - - -
205B ALA* 6.0 1.8 - - - +
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Residues in contact with GLN 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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164A ILE 4.7 3.4 + - - -
177A THR* 2.7 29.5 + - - +
178A HIS* 3.3 22.4 - - - +
179A ASN* 3.0 29.6 + - - +
192A ASN* 1.3 74.0 - - - +
194A PHE* 1.3 60.5 + - - +
195A VAL* 3.9 1.1 + - + +
217A TYR* 3.6 3.2 - - - -
218A LEU* 2.8 50.9 + - + +
224A ARG* 3.9 12.8 - - + +
225A LYS* 5.3 0.3 - - - -
227A CYS* 3.5 33.7 + - - +
238A MET* 4.0 18.2 - - + -
240A CYS* 5.0 0.2 - - - -
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Residues in contact with PHE 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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151A PHE 4.7 3.4 - - - -
153A PRO* 3.5 43.3 - - + -
176A TYR* 4.3 15.7 - + - -
177A THR* 2.6 28.2 + - - -
178A HIS* 2.8 35.4 + + + +
180A VAL* 4.3 4.9 - - + +
192A ASN 4.2 0.6 + - - -
193A GLN* 1.3 72.3 - - - +
195A VAL* 1.3 56.5 + - - +
196A SER* 3.6 24.7 - - - -
215A THR* 3.6 38.8 - - + -
216A LEU 3.6 11.9 - - - -
217A TYR* 4.1 10.9 - + + -
149B PRO* 4.1 15.7 - - + -
209B PHE* 4.5 11.2 - + - -
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Residues in contact with VAL 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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176A TYR 3.4 8.7 - - - +
177A THR* 3.7 4.5 - - - +
193A GLN 4.3 6.7 - - - +
194A PHE* 1.3 81.8 - - - +
196A SER* 1.3 66.8 + - - +
197A MET* 5.4 0.2 - - + -
215A THR* 3.3 4.2 - - - -
216A LEU* 2.7 51.9 + - + +
218A LEU* 4.7 5.4 - - + -
229A ILE* 4.1 11.2 - - + -
236A CYS* 5.1 4.7 - - - -
238A MET* 3.7 31.4 - - + -
264A MET* 3.7 33.4 - - + -
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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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151A PHE* 4.6 5.4 + - - -
174A TRP* 3.5 16.4 - - - -
175A CYS* 3.4 4.0 - - - +
176A TYR* 2.8 42.2 + - - +
194A PHE* 3.6 24.0 - - - -
195A VAL* 1.3 82.3 - - - +
197A MET* 1.3 64.4 + - - +
212A THR* 4.2 7.8 + - - -
214A LYS 3.2 13.7 - - - -
215A THR* 4.0 5.6 - - - -
216A LEU* 5.1 0.7 - - - -
236A CYS* 4.4 0.3 - - - -
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Residues in contact with MET 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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117A LEU* 4.1 19.5 - - + -
173A HIS* 4.8 2.2 - - + -
174A TRP* 3.3 20.0 - - - +
175A CYS* 4.4 0.7 - - - -
195A VAL* 5.4 0.9 - - + -
196A SER* 1.3 76.1 - - - +
198A GLY* 1.3 59.2 + - - +
212A THR* 3.7 1.9 - - - -
213A LEU 2.8 20.8 + - - -
214A LYS* 3.0 33.0 + - + +
216A LEU* 4.2 24.0 - - + -
235A GLY* 4.3 11.4 - - - -
236A CYS* 3.8 19.5 - - - -
264A MET* 3.7 27.4 - - + +
265A TYR 4.4 4.5 - - - +
266A TYR* 4.1 24.9 - - - -
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Residues in contact with GLY 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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117A LEU* 4.5 2.4 - - - +
173A HIS* 3.1 8.8 - - - +
174A TRP* 2.9 42.7 + - - -
197A MET* 1.3 76.4 - - - +
199A ILE* 1.3 64.1 + - - -
211A ARG 3.1 14.6 - - - -
213A LEU* 3.8 12.1 - - - -
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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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116A ALA 3.1 18.8 - - - +
117A LEU* 3.5 13.2 - - - -
118A ILE 3.4 39.9 - - - +
119A ASN* 3.2 11.0 - - - +
172A THR 3.8 3.8 - - - +
173A HIS* 4.2 0.9 - - + -
174A TRP* 2.9 11.2 + - - +
198A GLY* 1.3 80.2 - - - +
200A ILE* 1.3 63.9 + - - +
201A GLU* 4.8 6.7 - - + +
210A PHE 3.5 0.2 - - - -
211A ARG* 2.6 69.1 + - + +
213A LEU* 3.8 11.4 - - + -
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Residues in contact with ILE 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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119A ASN* 2.9 14.7 + - - +
120A ASP* 3.0 27.0 + - - +
123A TYR* 3.4 30.6 - - + -
127A ILE* 4.8 0.9 - - + -
169A LEU* 3.7 31.0 - - + -
174A TRP* 4.0 4.3 - - + -
199A ILE* 1.3 79.8 - - - +
201A GLU* 1.3 64.7 - - - +
208A PRO* 3.6 26.2 - - + -
209A PHE 3.3 8.1 - - - +
210A PHE* 3.8 29.8 - - + -
529A PHE* 4.2 13.0 - - + -
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Residues in contact with GLU 201 (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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120A ASP* 4.0 5.6 - - + +
123A TYR* 3.8 4.5 - - - -
199A ILE* 4.8 6.8 - - + +
200A ILE* 1.3 76.5 - - - +
202A PRO* 1.3 78.2 - - + +
208A PRO* 3.7 1.0 - - - +
209A PHE* 2.8 57.3 + - + +
211A ARG* 3.7 36.9 + - + -
216B LEU* 5.5 0.2 - - - -
217B TYR 4.3 14.6 + - - +
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Residues in contact with PRO 202 (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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120A ASP* 3.3 36.8 - - + +
122A ARG* 3.7 36.6 - - + +
123A TYR* 3.4 19.7 - - + +
201A GLU* 1.3 92.7 - - + +
203A THR* 1.3 64.7 + - - +
206A GLY 5.0 1.8 - - - +
207A PHE 3.9 2.0 - - - +
219B SER* 5.4 1.7 - - - +
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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