Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 1V1T
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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116A ILE* 4.0 25.1 - - + -
117A LEU 3.3 6.1 - - - +
118A CYS* 3.8 22.7 - - - -
162A ASN* 4.4 5.9 + - - +
182A PHE 4.2 11.6 - - - +
183A GLY* 4.6 0.6 - - - -
184A GLU* 1.3 84.7 - - + +
186A ILE* 1.3 61.5 + - - +
187A THR* 5.6 1.3 - - - +
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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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116A ILE* 3.3 4.4 - - - +
117A LEU* 2.7 43.8 + - + +
119A LYS* 3.3 42.0 - - + -
123A GLY 5.4 0.4 - - - +
125A ILE* 4.1 12.1 - - + -
161A ILE* 4.2 5.8 - - + -
162A ASN* 3.6 7.6 - - - +
178A LEU* 3.8 40.8 - - + +
181A ALA* 4.2 16.4 - - + -
185A LYS* 1.3 77.6 - - - +
187A THR* 1.3 75.6 + - - +
188A MET* 4.0 9.9 - - + -
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Residues in contact with THR 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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114A GLU* 3.5 37.9 + - + +
115A VAL 3.3 4.7 - - - +
116A ILE* 3.9 15.0 - - + +
161A ILE* 3.6 0.3 - - - -
162A ASN* 2.7 45.8 + - - +
163A GLY 5.7 1.8 - - - +
185A LYS* 4.3 1.1 - - - +
186A ILE* 1.3 77.7 - - - +
188A MET* 1.3 68.6 + - - +
189A THR* 5.3 2.0 - - - +
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Residues in contact with MET 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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114A GLU* 3.4 4.7 - - - +
115A VAL* 2.9 43.6 + - + +
117A LEU* 4.1 18.4 - - + -
125A ILE* 4.2 8.1 - - - -
127A LEU* 3.7 30.7 - - + -
129A LEU* 5.1 1.1 - - + -
152A LEU* 4.3 9.2 - - + -
158A VAL* 3.8 28.7 - - + -
160A GLN 3.3 11.0 - - - +
161A ILE* 4.1 16.6 - - + -
162A ASN 4.8 0.2 - - - +
178A LEU* 4.4 5.4 - - + -
186A ILE* 4.0 10.3 - - + -
187A THR* 1.3 80.6 - - - +
189A THR* 1.3 62.9 + - - +
190A ILE* 4.0 9.4 - - + -
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Residues in contact with THR 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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112A PRO* 3.8 24.9 - - + -
113A ARG 3.5 8.3 - - - +
114A GLU* 4.8 10.9 + - + +
158A VAL* 3.7 0.3 - - - -
159A LEU* 2.8 31.8 + - + -
160A GLN* 3.0 42.7 + - - +
187A THR* 5.3 1.6 - - - +
188A MET* 1.3 75.2 + - - +
190A ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 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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111A ASP 4.5 0.3 - - - +
112A PRO* 3.1 6.9 - - - +
113A ARG* 2.8 52.8 + - + +
115A VAL* 4.1 17.9 - - + -
152A LEU* 3.5 29.8 - - + -
156A ASP* 3.9 16.4 - - + +
157A GLN 3.3 5.6 - - - +
158A VAL* 3.9 26.0 - - + -
159A LEU* 4.9 0.7 - - - -
188A MET* 4.0 13.7 - - + +
189A THR* 1.3 81.9 - - - +
191A ARG* 1.3 74.4 + - - +
192A ASP* 3.9 14.0 + - - +
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Residues in contact with ARG 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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110A MET 4.5 18.0 + - - +
111A ASP 5.3 0.4 - - - -
112A PRO* 4.5 14.6 - - + +
156A ASP* 3.7 1.0 - - - -
157A GLN* 2.8 66.9 + - + +
159A LEU* 3.9 23.5 - - + +
189A THR 4.4 0.2 + - - -
190A ILE* 1.3 75.7 - - - +
192A ASP* 1.3 71.0 + - - +
194A PRO* 3.7 16.1 - - + +
197B ARG* 6.0 2.3 - - - +
199B ILE* 3.6 23.5 - - - +
230B ASN* 2.9 40.6 + - - +
231B GLY 3.8 4.0 + - - -
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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