Contacts of the strand formed by residues 188 - 199 (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 LEU 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ASP* 4.2 29.6 - - + +
159C ASN* 3.5 26.2 - - - +
161C PHE* 4.3 13.5 - - + -
180C VAL* 3.8 23.8 - - + -
182C ASN* 4.4 6.3 - - - +
187C PRO* 1.4 77.2 - - - +
189C GLU* 1.4 68.5 + - - +
190C ILE* 4.3 19.3 - - + -
293C VAL 3.5 1.6 - - - +
294C LEU* 3.5 7.6 - - - +
295C VAL* 2.9 48.3 + - + +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR 4.7 1.9 - - - +
116C GLY* 5.1 5.5 - - - -
117C ARG* 5.4 9.5 + - - +
188C LEU* 1.4 81.2 - - - +
190C ILE* 1.3 65.1 + - - +
292C PRO* 4.4 22.5 - - + +
293C VAL 3.5 6.1 - - - +
294C LEU* 4.0 23.2 - - + +
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Residues in contact with ILE 190 (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* 4.0 19.3 - - + -
115C THR 3.5 16.4 - - - +
116C GLY* 5.3 0.4 - - - -
118C ASP 4.8 1.6 - - - +
119C GLY* 3.6 25.6 - - - +
161C PHE* 4.2 13.7 - - + -
180C VAL* 3.8 20.9 - - + -
188C LEU* 4.3 15.3 - - + -
189C GLU* 1.3 79.4 - - - +
191C SER* 1.3 60.2 + - - +
192C SER 4.3 0.2 + - - -
292C PRO* 4.1 1.3 - - - -
293C VAL* 2.7 48.4 + - + +
295C VAL* 3.7 21.8 - - + -
303C MET* 4.0 13.0 - - + +
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 3.2 7.3 - - - -
115C THR* 2.7 59.7 + - - +
116C GLY* 4.8 2.2 - - - -
190C ILE* 1.3 73.6 - - - +
192C SER* 1.3 63.9 + - - +
289C LYS* 3.9 5.3 - - - +
290C SER 2.7 29.4 + - - -
291C GLN 4.8 0.4 - - - -
292C PRO* 4.3 16.6 - - - +
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Residues in contact with SER 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 3.7 10.6 - - - +
178C TYR* 3.1 16.5 - - - -
190C ILE 4.3 1.2 + - - -
191C SER* 1.3 72.6 + - - +
193C PHE* 1.4 59.8 + - - +
268C ASN* 3.3 24.5 + - - -
288C TYR* 3.0 23.1 + - - -
289C LYS* 3.4 3.1 - - - -
290C SER* 2.7 34.4 + - - +
291C GLN 5.3 0.8 + - - -
293C VAL* 5.8 0.8 - - - +
303C MET* 3.8 22.3 - - - +
304C ASN 5.1 0.2 + - - -
305C SER* 5.4 0.2 - - - -
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLN* 4.4 11.7 - - + -
112C SER 4.9 1.1 - - - -
113C GLY* 2.8 33.6 + - - +
114C LEU 4.4 0.2 - - - -
115C THR* 3.9 26.5 - - + +
121C ASP* 3.5 26.9 - - + -
123C PRO* 3.8 33.0 - - + -
178C TYR* 2.8 26.5 + - - -
192C SER* 1.4 80.2 + - - +
194C GLY* 1.3 61.2 + - - +
195C GLN* 3.8 26.9 - - + -
275C TYR* 3.3 23.6 - + - -
288C TYR* 3.5 21.6 - - - +
289C LYS* 5.1 1.6 - - + -
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Residues in contact with GLY 194 (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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111C GLN 3.6 5.4 - - - -
193C PHE* 1.3 80.0 - - - +
195C GLN* 1.4 60.8 - - - +
264C TRP* 3.2 27.4 - - - -
287C GLY* 3.1 2.3 - - - -
288C TYR* 3.0 40.5 + - - +
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Residues in contact with GLN 195 (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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111C GLN* 2.8 63.9 + - + +
123C PRO* 4.2 21.5 - - - +
193C PHE* 3.8 9.5 - - + -
194C GLY* 1.4 73.2 - - - -
196C LEU* 1.4 76.6 + - - +
197C LYS* 4.7 0.4 - - + +
264C TRP* 3.3 5.7 + - - -
275C TYR* 2.8 32.4 + - + +
279C LEU* 3.4 33.4 - - + +
285C ALA* 4.2 6.8 - - + +
286C ILE 3.6 7.2 - - - +
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Residues in contact with LEU 196 (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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109C GLN 3.4 6.3 - - - +
110C ALA* 3.6 22.0 - - + +
195C GLN* 1.4 84.6 - - - +
197C LYS* 1.3 58.2 + - - +
253C VAL* 3.4 31.0 - - + +
254C ALA* 4.2 8.7 - - - -
255C MET* 3.4 20.3 - - + +
262C THR* 4.2 12.6 - - + +
263C ALA* 3.7 16.2 - - - -
264C TRP* 3.5 24.9 - - + +
285C ALA* 3.2 4.0 - - - +
286C ILE* 2.8 40.2 + - + +
307C LEU* 4.1 9.0 - - + -
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Residues in contact with LYS 197 (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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107C ILE* 3.9 35.7 - - + +
108C TYR* 3.3 4.4 - - - -
109C GLN* 3.0 60.2 + - + +
111C GLN* 3.4 29.7 - - + +
195C GLN* 4.8 0.7 - - + -
196C LEU* 1.3 74.8 - - - +
198C GLN* 1.4 59.6 + - - +
255C MET* 4.3 0.6 - - - +
279C LEU* 4.0 23.0 + - + +
283C ILE* 4.3 10.0 - - + +
284C ALA 3.6 4.3 - - - +
285C ALA* 3.9 13.9 - - + -
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Residues in contact with GLN 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PHE* 5.2 2.0 - - + -
107C ILE 3.4 4.0 - - - -
108C TYR* 3.7 32.4 - - + -
197C LYS* 1.4 73.5 - - - +
199C SER* 1.4 72.4 + - - +
200C ILE 3.6 0.2 + - - -
219C ARG* 3.1 34.5 + - - +
220C GLY 3.8 6.3 + - - -
235C PHE* 3.6 25.9 - - + -
255C MET* 3.6 39.5 - - + +
256C LEU 4.3 5.2 + - - +
257C GLN* 4.9 1.0 - - - +
283C ILE* 4.1 4.1 - - - +
284C ALA 2.9 34.7 + - - +
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Residues in contact with SER 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PHE* 3.2 40.6 - - - -
107C ILE 2.7 27.6 + - - -
198C GLN* 1.4 76.8 - - - +
200C ILE* 1.4 64.7 + - - +
201C THR* 3.3 5.0 + - - -
219C ARG* 4.5 1.9 - - - -
235C PHE* 3.3 14.0 - - - -
282C GLY 3.5 8.4 + - - -
283C ILE* 3.9 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