Contacts of the strand formed by residues 168 - 177 (chain C) in PDB entry 5FJV
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 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.7 11.0 - - - +
164C PHE* 4.3 19.7 - - + +
165C PRO* 3.6 47.6 + - + +
166C PHE 3.3 0.8 - - - -
167C ASP* 1.3 79.2 + - - +
169C GLN* 1.3 78.5 + - - +
170C ASN* 5.7 0.8 - - - +
234C VAL* 3.7 21.3 - - - +
235C ILE 3.3 6.3 - - - -
236C ARG* 2.7 53.6 + - + +
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Residues in contact with GLN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C VAL* 4.3 21.4 - - - +
74C GLU* 4.6 24.4 + - - +
77C GLN* 5.4 6.8 - - - +
157C CYS* 4.4 13.2 - - - +
158C SER* 4.0 17.2 - - - +
159C ILE* 4.3 17.4 + - + +
166C PHE 5.3 0.7 - - - +
167C ASP 5.1 2.6 - - - +
168C GLN* 1.3 93.7 - - - +
170C ASN* 1.3 60.9 + - - +
171C CYS* 4.4 6.1 - - - -
233C PHE 3.7 0.2 - - - +
234C VAL* 3.2 6.0 - - - +
235C ILE* 2.7 55.9 + - + +
237C ARG* 4.7 7.9 - - + +
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Residues in contact with ASN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C CYS* 3.1 1.0 - - - +
158C SER* 2.9 43.2 + - - +
159C ILE* 4.9 0.8 - - - +
160C ASP* 5.8 6.3 - - + +
164C PHE* 6.5 0.7 - - + -
168C GLN* 5.7 1.0 - - - +
169C GLN* 1.3 72.8 - - - +
171C CYS* 1.3 59.3 + - - +
172C LYS* 2.8 41.9 + - - +
232C ALA* 4.2 6.9 - - - +
233C PHE 2.3 37.6 + - - +
234C VAL* 3.7 12.9 - - + +
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Residues in contact with CYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C MET* 3.5 26.0 - - + -
157C CYS* 2.0 45.3 - - + -
169C GLN* 3.8 7.4 + - - -
170C ASN* 1.3 74.4 - - - +
172C LYS* 1.3 60.9 + - - +
233C PHE* 2.8 50.5 + - + -
235C ILE* 3.8 27.1 - - + -
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASN* 2.8 32.4 - - - +
155C SER* 3.2 9.7 + - - -
156C SER 3.7 3.2 + - - +
157C CYS* 4.0 5.3 - - - +
158C SER* 5.8 5.5 - - - +
170C ASN* 2.8 32.8 + - - +
171C CYS* 1.3 71.7 - - - +
173C MET* 1.3 57.7 - - - +
230C THR* 4.4 15.7 - - + -
231C TYR 3.1 4.5 - - - +
232C ALA* 3.8 20.0 - - + -
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Residues in contact with MET 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 4.3 9.0 - - - -
79C MET* 4.3 9.6 - - + -
81C THR* 3.6 28.5 - - - +
83C VAL* 4.9 3.4 - - + -
121C LEU* 3.8 17.0 - - + -
123C ASN* 4.1 4.5 - - - -
153C TYR* 3.7 26.7 - - + -
155C SER* 4.0 15.7 - - - +
172C LYS* 1.3 79.2 - - - +
174C LYS* 1.3 60.8 + - - +
175C PHE* 3.6 16.9 + - + -
229C VAL 3.9 0.3 - - - +
230C THR* 3.4 2.8 - - - -
231C TYR* 2.6 42.9 + - + +
233C PHE* 3.8 29.4 - - + -
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Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 3.5 3.2 - - - +
122C TYR* 2.6 73.5 + - + +
123C ASN* 3.7 20.5 - - - +
173C MET* 1.3 72.1 - - - +
175C PHE* 1.3 56.4 + - - +
217C LYS* 4.6 7.9 - - - +
219C TYR* 2.2 39.1 + - - -
228C ASP* 3.3 30.5 + - + +
229C VAL 3.9 0.7 - - - -
230C THR* 3.5 25.8 - - + +
201D GLU* 5.9 2.9 - - - +
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 3.6 32.6 - + + -
64C LEU* 3.7 32.1 - - + -
83C VAL* 4.9 1.3 - - + -
85C LEU* 4.0 17.9 - - + -
119C ILE* 4.3 1.6 - - + -
120C VAL 3.4 15.9 - - - -
121C LEU* 3.4 24.5 - - + -
122C TYR* 4.2 3.4 - - - -
153C TYR* 3.2 44.0 - + - -
173C MET* 4.0 21.1 - - + -
174C LYS* 1.3 72.6 - - - +
176C GLY* 1.3 58.2 + - - +
187C LEU* 5.0 0.9 - - - +
228C ASP* 3.4 2.9 - - - -
229C VAL* 2.8 41.2 + - - +
231C TYR* 4.5 4.0 - + - -
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Residues in contact with GLY 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 3.9 10.1 - - - +
120C VAL* 2.8 35.7 + - - +
122C TYR* 3.9 11.6 - - - -
175C PHE* 1.3 76.8 - - - +
177C SER* 1.3 67.1 + - - -
187C LEU* 4.5 6.5 - - - -
227C PRO 4.0 11.2 - - - -
228C ASP* 4.4 0.7 - - - -
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASP* 2.8 22.9 + - - -
119C ILE* 3.8 19.2 - - - +
122C TYR* 3.2 18.5 + - - -
176C GLY* 1.3 70.8 - - - -
178C TRP* 1.3 59.9 + - - +
180C TYR* 3.0 42.8 + - - +
185C ILE* 4.4 12.8 - - - -
187C LEU* 4.5 4.9 - - - +
226C TYR* 4.7 3.1 - - - +
227C PRO* 4.2 10.0 + - - +
300C EPJ 4.2 1.4 + - - -
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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