Contacts of the helix formed by residues 167 - 177 (chain C) in PDB entry 1XFV
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 LYS 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C PHE* 3.1 40.2 - - + -
160C ALA* 3.0 35.7 + - - +
161C ILE* 3.4 22.7 - - + +
164C GLU* 2.8 37.3 + - - +
165C GLN 2.5 9.5 + - - -
166C SER* 1.3 76.2 - - - +
168C GLU* 1.3 63.8 + - - +
169C VAL 3.5 0.2 - - - -
170C TYR* 3.9 8.5 - - - +
171C TYR 4.3 0.5 + - - -
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Residues in contact with GLU 168 (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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84C ASP 4.9 0.5 - - - +
85C LEU* 2.8 26.8 - - + +
88C LYS* 2.7 35.5 + - - +
141C PHE* 5.5 0.4 - - - -
161C ILE* 3.0 31.5 - - + +
162C ASN* 4.9 2.1 - - - +
165C GLN 2.5 15.2 + - - +
167C LYS* 1.3 72.4 - - - +
169C VAL* 1.3 52.9 + - - +
170C TYR 2.5 18.1 + - - -
171C TYR* 2.7 20.2 + - + +
172C GLU* 3.0 20.6 + - - +
251C PRO* 3.3 27.1 - - + +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ARG* 4.5 21.5 - - - +
165C GLN 3.2 7.5 + - - +
166C SER* 3.2 32.3 - - - +
168C GLU* 1.3 74.5 - - - +
170C TYR* 1.3 64.2 + - + +
172C GLU* 3.8 7.6 - - - -
173C ILE* 2.8 27.4 + - + +
246C SER* 3.6 25.2 - - - +
247C TYR* 4.5 7.0 - - + -
250C ALA* 4.4 8.9 - - + +
251C PRO* 5.8 0.6 - - - +
252C ASP* 5.7 0.6 + - - +
253C HIS* 3.5 33.9 - - + +
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Residues in contact with TYR 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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130C SER* 2.8 24.4 + - - -
131C ARG* 2.6 56.5 + - + +
140C ARG* 3.1 34.8 - - - +
141C PHE* 4.4 6.5 - + + -
142C VAL* 5.0 3.6 - - + -
166C SER 4.4 13.7 - - - -
167C LYS* 3.9 12.1 + - - +
168C GLU 2.5 6.5 + - - -
169C VAL* 1.3 76.3 - - + +
171C TYR* 1.3 53.6 + - - +
172C GLU 2.5 11.9 + - - -
173C ILE* 3.4 16.4 - - + -
174C GLY* 2.4 36.8 + - - -
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Residues in contact with TYR 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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85C LEU* 3.3 38.6 - - + -
86C LEU* 3.0 26.0 - - - +
88C LYS* 3.9 3.4 - - - -
89C ILE* 3.9 8.6 - - + +
104C ILE* 3.5 13.9 - - - +
106C PHE* 3.5 8.6 - + - -
141C PHE* 5.2 2.9 - - + -
142C VAL* 3.7 23.5 - - + +
152C LEU* 3.6 14.1 - - + +
154C ILE* 3.1 45.8 - - + -
161C ILE* 6.5 0.7 - - + -
167C LYS 4.3 2.1 + - - +
168C GLU* 2.7 16.3 + - + +
170C TYR* 1.3 74.4 - - - +
172C GLU* 1.3 64.1 + - - +
174C GLY 4.3 0.7 - - - -
175C LYS* 2.7 45.6 + - - +
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Residues in contact with GLU 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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88C LYS* 2.3 51.3 + - + +
89C ILE* 4.4 3.9 - - + +
168C GLU* 3.0 19.5 + - - +
169C VAL* 3.7 11.7 - - - +
170C TYR 2.5 5.7 + - - -
171C TYR* 1.3 86.6 - - - +
173C ILE* 1.3 60.2 + - - +
175C LYS* 3.0 25.3 + - - +
176C GLY 3.3 3.6 + - - -
245C PHE* 3.4 19.6 - - + -
246C SER* 4.0 17.7 - - - +
249C PHE* 4.4 19.3 - - + -
250C ALA* 4.5 1.8 - - - +
251C PRO* 3.9 9.2 - - - +
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Residues in contact with ILE 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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130C SER* 4.6 21.3 - - - +
131C ARG* 4.7 2.0 - - + +
169C VAL* 2.8 20.4 + - + +
170C TYR* 3.4 22.9 - - + -
172C GLU* 1.3 71.2 - - - +
174C GLY* 1.3 65.1 + - - +
175C LYS 2.3 19.4 + - - +
176C GLY* 2.6 17.2 + - - +
177C ILE* 3.6 7.6 + - + +
239C HIS* 5.0 4.9 - - - +
242C SER* 3.3 39.5 - - - +
243C LEU* 3.1 31.0 - - + -
246C SER* 3.8 6.7 - - - +
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Residues in contact with GLY 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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142C VAL* 4.5 16.9 - - - +
143C PHE 5.8 0.2 - - - -
144C GLU* 4.3 10.9 + - - +
152C LEU* 5.1 1.9 - - - +
170C TYR* 2.4 25.3 + - - -
173C ILE* 1.3 77.0 - - - +
175C LYS* 1.3 54.2 + - - +
177C ILE* 3.0 29.1 - - - +
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Residues in contact with LYS 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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89C ILE* 3.8 22.3 - - + +
93C VAL* 4.3 13.0 - - + -
94C LEU* 5.3 2.2 - - + -
97C TYR* 4.1 11.0 - - + -
104C ILE* 4.6 4.0 - - - -
144C GLU* 4.9 0.6 - - - +
152C LEU* 3.6 27.6 - - + +
171C TYR* 2.7 39.5 + - - -
172C GLU* 3.0 12.6 + - - +
173C ILE 2.3 13.4 + - - -
174C GLY* 1.3 70.0 - - - +
176C GLY* 1.3 53.2 - - - +
177C ILE* 2.3 21.3 + - - +
178C SER* 2.4 35.3 + - - +
179C LEU* 4.4 1.3 - - + -
245C PHE* 4.2 21.7 - - + -
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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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172C GLU 3.3 5.1 + - - -
173C ILE 2.6 11.3 + - - -
175C LYS* 1.3 74.4 - - - +
177C ILE* 1.3 47.9 + - - -
178C SER* 2.7 4.0 - - - -
179C LEU* 2.6 22.0 + - - +
180C ASP* 2.5 30.4 + - - +
241C PHE* 4.9 2.8 - - - -
242C SER* 4.0 15.3 - - - -
245C PHE* 4.6 13.2 - - - -
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Residues in contact with ILE 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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129C ASN 6.1 0.7 - - - +
144C GLU* 4.4 22.1 - - + +
173C ILE* 3.6 5.7 + - + +
174C GLY* 3.0 32.3 - - - +
175C LYS 2.3 10.8 + - - -
176C GLY* 1.3 63.4 - - - -
178C SER* 1.3 53.7 + - - -
180C ASP* 2.7 29.9 - - - +
181C ILE* 4.5 7.4 - - - +
238C GLN* 4.6 11.0 - - + +
239C HIS* 5.8 8.7 - - + +
242C SER* 3.8 16.3 + - - +
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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