Contacts of the strand formed by residues 183 - 189 (chain A) in PDB entry 1GC5
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 ILE 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.5 20.9 - - + +
43A ALA* 3.6 30.7 - - + +
109A ARG* 3.8 15.0 - - - +
113A TRP* 4.5 13.5 - - + -
116A LEU* 5.5 0.2 - - + -
147A LEU* 5.3 1.8 - - + -
181A GLU* 3.5 36.9 + - + +
182A LEU* 1.3 72.8 - - - +
184A HIS* 1.3 71.5 + - - +
185A TYR* 3.9 31.3 + - + +
210A ALA* 3.3 34.8 + - + +
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Residues in contact with HIS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 3.3 29.0 + - - -
41A ILE 2.8 12.6 + - - +
42A ASP* 3.5 12.4 - - - +
43A ALA 2.9 22.0 + - - -
96A GLU* 4.5 6.1 - - - -
120A GLY 5.9 0.4 - - - -
182A LEU 4.1 0.2 + - - -
183A ILE* 1.3 80.0 + - - +
185A TYR* 1.3 62.2 + - - +
186A ILE* 3.4 4.8 + - + +
207A ILE* 4.2 16.2 - - + -
208A ALA 3.7 4.7 - - - -
209A ASN* 2.8 28.9 + - + +
211A ASP* 2.9 43.7 + - + -
214A ASN* 5.4 2.4 - - - +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.3 21.8 - - + +
105A ARG* 4.1 4.5 + - - +
108A LEU* 3.4 51.6 - - + +
109A ARG* 3.7 22.7 + - - +
112A GLY 5.0 4.3 - - - -
113A TRP* 3.9 20.8 - + + -
183A ILE* 3.9 37.5 - - + +
184A HIS* 1.3 69.8 - - - +
186A ILE* 1.3 62.2 + - - +
187A TYR* 3.7 29.9 - + + +
206A PHE 3.5 2.1 - - - +
207A ILE* 3.4 3.5 - - - -
208A ALA* 2.9 43.4 + - + +
210A ALA* 4.3 11.0 - - + -
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 3.5 35.9 - - + +
43A ALA 2.7 11.9 + - - +
44A ILE* 3.3 13.3 - - + +
45A LYS 2.9 27.7 + - - +
184A HIS* 3.8 9.4 - - + +
185A TYR* 1.3 74.8 - - - +
187A TYR* 1.3 64.4 + - - +
188A GLU* 3.8 16.4 - - - +
205A ARG* 3.7 31.4 - - + -
206A PHE 3.7 2.2 - - - -
207A ILE* 3.8 25.1 - - + +
447A VAL* 4.3 17.5 - - + -
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 3.4 47.6 - - + -
47A LEU* 3.8 25.8 - - + -
81A LEU* 4.6 6.3 - - + -
85A ILE* 4.3 19.5 - - + -
108A LEU* 3.3 27.9 + - + +
111A TRP* 3.6 24.9 - + - +
112A GLY 4.9 1.9 + - - -
185A TYR* 3.7 39.2 - + + +
186A ILE* 1.3 71.1 - - - +
188A GLU* 1.3 60.9 + - - +
189A PHE* 4.4 4.0 - - - -
205A ARG* 3.0 5.2 - - - -
206A PHE* 2.8 47.3 + + + +
208A ALA* 4.3 10.3 - - + -
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.4 26.7 - - + +
45A LYS 3.4 4.3 + - - +
46A TYR* 3.0 39.0 + - + +
47A LEU* 3.2 25.6 + - - +
186A ILE* 3.8 15.3 - - + +
187A TYR* 1.3 76.6 - - - +
189A PHE* 1.3 61.7 + - - +
190A PRO* 4.7 1.0 - - - +
203A GLU* 3.7 11.2 - - - +
204A ASN 3.5 12.6 - - - +
205A ARG* 4.3 6.2 - - + +
444A LYS 5.5 2.8 - - - +
445A SER* 4.7 8.7 - - - +
446A THR* 5.9 0.7 - - - +
447A VAL* 4.2 14.3 - - - +
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.0 8.7 - - + -
85A ILE* 4.4 1.1 - - + -
88A SER* 3.0 44.9 - - - -
89A ILE* 3.5 28.9 - - + -
92A GLY* 4.7 1.1 - - - -
187A TYR 4.4 3.4 - - - -
188A GLU* 1.3 77.1 - - - +
190A PRO* 1.3 73.3 - - + +
193A PHE* 3.7 23.3 - - + -
200A ALA* 4.1 8.3 - - + -
202A ARG 3.5 13.0 - - - -
203A GLU* 2.8 23.1 - - - +
204A ASN* 3.1 39.3 + - + -
205A ARG* 4.0 9.0 - - - -
206A PHE* 4.6 1.3 - - + -
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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