Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 2GWU
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ILE* 3.0 5.4 - - - -
165A ARG* 2.6 45.8 + - + +
166A ARG 3.5 21.3 - - - +
167A GLU* 4.2 5.8 - - + -
168A GLN* 3.6 37.8 + - - +
182A GLU* 5.1 9.0 - - + +
183A ASP 4.8 3.8 - - - +
184A SER* 1.3 77.1 - - - +
186A TYR* 1.4 64.3 + - - +
187A ARG* 4.5 13.5 - - - +
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Residues in contact with TYR 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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142A ASP* 4.6 15.9 + - - -
151A ARG* 3.8 44.9 + - + +
162A ASP* 5.1 9.0 - - + -
163A GLN 3.6 0.7 - - - +
164A ILE* 3.0 31.2 - - + -
183A ASP* 6.5 0.4 - - + -
184A SER 4.9 5.4 - - - -
185A LYS* 1.4 73.6 - - - +
187A ARG* 1.3 72.7 + - - +
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Residues in contact with ARG 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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95A SER* 6.6 0.2 - - - -
96A THR* 3.7 35.5 - - - +
97A PRO* 5.4 2.2 - - - +
162A ASP* 3.0 6.1 - - - -
163A GLN* 2.8 51.7 + - - +
165A ARG* 3.0 53.7 - - + +
185A LYS* 4.5 13.7 - - - +
186A TYR* 1.3 91.7 + - - +
188A LYS* 1.4 60.2 + - - +
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Residues in contact with LYS 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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94A TYR* 3.3 51.4 - - + +
95A SER* 3.3 22.2 - - - -
96A THR 4.5 1.2 + - - -
97A PRO* 5.6 0.2 - - - +
160A TYR* 3.0 52.5 - - + -
161A LEU 3.5 7.9 - - - +
162A ASP* 2.7 20.4 - - - +
163A GLN* 4.3 0.7 - - - -
187A ARG* 1.4 73.9 - - - +
189A ILE* 1.4 56.5 + - - +
190A TYR 4.2 5.6 - - - +
191A SER* 4.1 6.3 - - - -
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Residues in contact with ILE 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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93A VAL* 3.4 3.1 - - - +
94A TYR 2.9 19.6 + - - -
95A SER* 3.1 27.0 + - - -
125A PHE* 2.9 49.4 - - + -
129A TYR* 5.3 7.0 - - + +
161A LEU* 2.9 33.8 + - + +
163A GLN* 3.3 27.4 - - - +
187A ARG 3.6 3.6 + - - -
188A LYS* 1.4 71.1 - - - +
190A TYR* 1.4 95.7 + - + +
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Residues in contact with TYR 190 (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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91A GLY* 5.3 0.7 - - - -
92A TYR 2.9 22.0 - - - +
93A VAL* 3.7 8.7 - - + -
94A TYR 3.9 3.1 - - - +
107A HIS* 3.5 31.6 - + + -
109A LEU* 3.4 13.6 - - + +
122A ASP* 3.1 18.9 + - - -
125A PHE* 3.8 10.1 - + + -
131A MET* 3.3 11.6 - - - +
160A TYR* 3.4 2.8 - - - +
161A LEU* 2.9 55.1 + - + +
188A LYS* 3.8 7.8 - - - +
189A ILE* 1.4 112.2 - - + +
191A SER* 1.4 60.8 + - - +
192A PHE* 3.7 28.7 - + + -
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Residues in contact with SER 191 (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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91A GLY* 3.0 4.5 - - - -
92A TYR* 2.8 54.7 + - - +
94A TYR* 5.7 0.5 - - - +
158A PHE* 3.8 8.8 - - - -
159A TRP 3.0 6.1 - - - -
160A TYR* 3.1 35.4 - - - -
188A LYS* 4.1 4.3 + - - +
190A TYR* 1.4 75.1 - - - +
192A PHE* 1.3 63.4 + - - +
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Residues in contact with PHE 192 (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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89A LEU* 3.9 17.9 - - + -
90A GLY 3.2 19.5 - - - +
91A GLY* 3.8 3.8 - - - -
109A LEU* 4.1 9.0 - - + -
120A ILE* 4.1 6.1 - - + -
137A LEU* 3.6 30.1 - - + -
152A LEU* 4.1 18.6 - - + -
158A PHE* 3.5 12.3 - - - -
159A TRP* 2.8 72.9 + + + -
161A LEU* 4.6 3.4 - - + -
190A TYR* 3.7 30.1 - + + -
191A SER* 1.3 76.7 - - - +
193A THR* 1.3 71.9 + - - +
194A LEU* 4.6 1.1 - - + -
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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