Contacts of the strand formed by residues 173 - 181 (chain C) in PDB entry 5MG3
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 ALA 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C LEU* 5.2 0.3 - - - +
166C VAL 4.8 1.0 - - - +
168C LYS* 3.5 24.1 + - - +
171C ASP* 3.5 20.2 + - - +
172C TYR* 1.3 79.1 - - - +
174C VAL* 1.4 62.2 + - - +
175C ASN 3.9 0.4 - - - -
306C THR* 3.7 20.6 - - + -
307C LEU 3.8 4.7 - - - -
308C TRP* 3.7 23.8 - - + -
320C VAL* 5.4 9.6 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.0 22.0 - - + -
70C LEU* 4.5 11.4 - - + -
165C PHE* 4.1 24.7 - - + -
166C VAL 3.5 20.4 - - - +
167C LEU* 3.9 26.2 - - + -
172C TYR 3.8 0.2 + - - -
173C ALA* 1.4 71.8 - - - +
175C ASN* 1.4 69.1 + - - +
176C VAL* 3.4 3.8 + - + -
306C THR* 4.2 0.7 - - - -
307C LEU* 2.7 49.8 + - + +
309C VAL* 4.8 4.0 - - + -
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Residues in contact with ASN 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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146C GLU* 5.7 2.6 + - - -
164C THR 3.6 1.7 - - - +
166C VAL* 2.9 47.8 + - + +
168C LYS* 5.0 16.9 + - - +
173C ALA 3.9 2.6 + - - -
174C VAL* 1.4 69.1 - - - +
176C VAL* 1.4 60.1 + - - +
177C ASN* 4.1 13.2 + - - +
267C HIS* 5.3 1.8 + - - -
305C SER 3.6 5.8 - - - +
306C THR* 2.8 28.2 + - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C SER* 4.3 10.5 - - - -
163C LYS* 5.2 1.6 - - + -
164C THR 3.4 11.4 - - - +
165C PHE* 4.0 22.7 - - + -
174C VAL* 3.4 12.1 + - + +
175C ASN* 1.4 76.2 - - - +
177C ASN* 1.4 64.6 + - - +
178C TYR* 3.5 37.2 + - + +
264C TRP* 3.8 27.6 - - + -
303C MET 4.2 0.2 - - - +
304C ASN* 3.8 1.2 - - - -
305C SER* 2.9 35.0 + - - +
307C LEU* 3.9 8.1 - - + +
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Residues in contact with ASN 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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162C THR 4.0 1.0 - - - +
163C LYS* 3.6 0.9 - - - -
164C THR* 2.8 44.5 + - - +
166C VAL* 4.3 17.3 - - - +
175C ASN* 4.1 13.3 + - - +
176C VAL* 1.4 76.5 - - - +
178C TYR* 1.3 59.4 + - - +
179C ASN* 4.3 11.5 + - - +
303C MET 3.8 7.0 - - - +
304C ASN* 4.5 14.3 - - - +
305C SER 4.7 0.7 - - - +
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Residues in contact with TYR 178 (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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112C SER* 3.6 4.7 - - - -
113C GLY* 3.0 37.8 + - - -
114C LEU* 3.6 26.0 - - + -
162C THR 3.5 3.6 - - - -
163C LYS* 4.2 15.3 - - + -
176C VAL* 3.5 24.7 - - + -
177C ASN* 1.3 72.5 - - - +
179C ASN* 1.3 64.6 + - - +
192C SER* 3.1 30.1 - - - -
193C PHE 2.8 17.3 + - - -
264C TRP* 3.6 21.0 - - - -
288C TYR* 3.6 10.3 + - - -
302C ALA* 3.7 2.3 - - - +
303C MET* 3.1 42.7 + - - +
304C ASN 4.7 1.1 - - - -
305C SER* 4.4 9.0 - - - -
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Residues in contact with ASN 179 (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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114C LEU* 3.9 7.8 - - - +
160C THR 4.6 0.2 - - - -
161C PHE* 3.5 3.6 - - - -
162C THR* 2.9 45.4 + - - +
164C THR* 5.1 4.5 + - - -
177C ASN* 4.3 14.4 - - - +
178C TYR* 1.3 73.7 - - - +
180C VAL* 1.4 62.3 + - - +
181C GLN* 4.3 5.8 - - + +
300C THR* 4.4 14.8 - - + +
301C GLY 3.3 15.5 + - - +
302C ALA* 3.8 17.0 - - - +
303C MET* 5.2 0.4 - - - -
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Residues in contact with VAL 180 (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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114C LEU* 3.6 26.2 - - + -
159C ASN* 4.4 2.7 - - + -
160C THR 3.5 4.3 - - - +
161C PHE* 3.7 30.5 - - + +
179C ASN* 1.4 71.5 - - - +
181C GLN* 1.4 73.6 + - - +
182C ASN* 4.0 3.4 - - + +
188C LEU* 3.8 18.2 - - + -
190C ILE* 3.8 22.9 - - + -
295C VAL* 4.5 9.1 - - + +
299C GLN 4.2 0.9 - - - +
300C THR* 3.4 3.6 - - - +
301C GLY 2.8 35.6 + - - +
303C MET* 4.3 4.9 - - + +
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Residues in contact with GLN 181 (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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159C ASN* 3.6 5.5 - - - +
160C THR* 2.9 59.4 + - - +
162C THR* 5.0 5.1 + - - -
179C ASN* 5.7 5.6 - - + +
180C VAL* 1.4 72.4 - - - +
182C ASN* 1.3 57.2 + - - +
183C ALA* 3.2 10.2 + - + +
299C GLN 3.9 5.2 - - - -
300C THR* 3.7 28.4 - - + +
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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