Contacts of the strand formed by residues 173 - 178 (chain C) in PDB entry 3GXM
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 SER 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LYS* 3.3 28.7 + - - -
117C ASN* 2.7 14.1 + - - -
118C ILE* 3.2 14.2 - - - +
119C ILE 3.1 21.0 + - - -
171C PRO 4.0 0.7 + - - -
172C VAL* 1.3 72.5 - - - +
174C LEU* 1.3 61.4 + - - +
228C TRP* 3.5 28.6 - - - +
429C GLU* 4.6 6.6 + - - -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ILE* 3.4 24.2 - - + +
121C VAL* 4.6 4.9 - - + -
161C ILE* 3.9 32.5 - - + -
165C LEU* 4.3 8.1 - - + -
172C VAL* 4.0 15.7 + - + +
173C SER* 1.3 76.3 - - - +
175C LEU* 1.3 58.0 + - - +
225C LEU* 4.1 24.7 - - + -
226C GLN 3.6 22.3 + - - +
227C PHE* 3.4 31.9 - - + -
228C TRP* 2.8 32.6 + - - +
229C ALA 3.4 4.7 + - - -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 4.7 4.0 - - + -
119C ILE 2.8 14.2 + - - +
120C ARG* 3.2 27.8 - - + +
121C VAL 2.6 32.6 + - - -
173C SER 3.9 0.2 + - - -
174C LEU* 1.3 73.9 - - - +
176C ALA* 1.3 57.8 + - - +
227C PHE* 4.0 2.2 - - - -
228C TRP* 4.1 11.4 - - + -
229C ALA* 3.4 35.9 - - + +
230C VAL* 3.9 12.6 - - - +
231C THR* 4.0 11.9 - - + -
279C LEU* 4.1 6.5 - - + -
337C PHE* 3.9 28.9 - - + -
339C SER* 4.2 16.2 - - - +
379C THR* 4.8 1.8 - - - +
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL 3.2 10.8 - - - +
123C MET* 4.0 8.1 - - + -
175C LEU* 1.3 73.0 - - - +
177C SER* 1.3 63.2 + - - +
178C PRO* 4.4 0.3 - - - +
216C PHE* 3.7 19.7 - - + -
227C PHE* 3.5 22.6 - - + -
229C ALA 3.1 7.9 + - - -
230C VAL* 3.1 17.9 - - + +
231C THR 2.8 26.9 + - - +
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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
----------------------------------------------------------
120C ARG* 3.1 39.2 + - - +
121C VAL 3.5 5.9 + - - -
122C PRO* 3.4 5.5 - - - +
123C MET* 2.9 23.3 + - - -
175C LEU* 4.1 1.5 + - - +
176C ALA* 1.3 75.2 + - - +
178C PRO* 1.4 66.7 - - - +
179C TRP* 3.5 6.9 - - - -
231C THR* 3.0 26.6 + - - +
234C ASN* 3.9 8.5 - - - -
282C ASP* 3.2 2.3 + - - -
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Residues in contact with PRO 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C MET* 3.3 30.3 - - + +
177C SER* 1.4 83.6 - - - +
179C TRP* 1.4 58.9 + - - +
180C THR 4.7 1.6 - - - +
209C TRP* 3.6 31.6 - - + -
213C PHE* 3.5 23.6 - - + -
231C THR 3.3 19.7 - - - +
232C ALA 4.0 7.4 - - - +
233C GLU* 3.5 7.9 - - - +
234C ASN* 2.8 30.8 + - - +
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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