Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 1INL
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 PHE 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS* 3.8 22.0 - - + +
94A VAL 4.0 6.7 - - - -
95A LEU* 3.8 48.0 - - + -
118A ILE* 3.8 30.5 - - + -
160A PHE* 3.8 42.8 - + + -
163A GLU* 1.3 85.8 - - + +
165A ASP* 1.3 63.0 + - - +
166A VAL 3.9 11.4 - - - +
167A ILE* 4.2 9.0 - - + -
194A ALA* 3.0 22.4 + - + +
195A LEU* 3.3 7.0 - - + +
196A LYS* 2.9 31.0 + - - +
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Residues in contact with ASP 165 (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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88A HIS* 3.2 36.3 + - + +
90A ASN 4.2 2.0 - - - +
91A PRO* 4.1 9.9 - - + -
92A LYS* 2.9 32.7 + - - +
93A LYS* 2.8 24.2 + - - +
164A PHE* 1.3 75.8 - - - +
166A VAL* 1.3 59.7 + - + +
195A LEU* 3.7 1.6 - - - -
196A LYS* 3.5 26.8 - - - +
198A ASP* 5.0 1.6 - - - +
199A GLY* 3.2 7.0 - - - -
200A VAL 3.0 24.6 + - - -
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Residues in contact with VAL 166 (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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84A PRO* 4.2 10.3 - - + +
85A MET* 4.0 13.5 - - - -
88A HIS* 4.2 4.5 - - + -
91A PRO* 3.9 27.1 - - + -
93A LYS 3.3 2.2 + - - -
94A VAL* 3.4 13.8 - - + -
95A LEU 2.9 24.9 + - - -
164A PHE* 3.9 1.9 - - - +
165A ASP* 1.3 87.8 - - + +
167A ILE* 1.3 69.8 + - - +
168A ILE* 3.9 27.8 - - + -
195A LEU* 4.0 0.2 - - - -
200A VAL* 3.4 28.3 - - + +
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Residues in contact with ILE 167 (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 LEU* 3.3 19.3 - - + +
97A ILE* 4.7 6.7 - - + -
157A VAL* 4.3 6.7 - - + -
164A PHE* 4.2 9.4 - - + -
166A VAL* 1.3 80.2 - - - +
168A ILE* 1.3 65.1 + - - +
169A ILE* 3.9 23.6 - - + -
191A CYS* 3.5 37.9 - - - +
194A ALA* 4.0 16.6 - - + -
195A LEU* 3.7 16.2 - - + -
200A VAL 3.2 5.3 + - - -
201A PHE* 3.3 20.5 - - + -
202A SER 3.1 23.2 + - - +
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Residues in contact with ILE 168 (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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80A LEU* 3.6 36.8 - - + -
81A ALA* 4.1 18.8 - - - +
84A PRO* 4.3 3.6 - - + -
85A MET* 4.8 1.1 - - + -
94A VAL* 4.4 4.7 - - + -
95A LEU 2.9 12.8 + - - +
96A ILE* 3.3 7.3 - - + +
97A ILE 2.9 25.5 + - - -
104A THR* 3.9 12.1 - - + -
108A VAL* 3.8 29.2 - - + -
166A VAL* 3.9 21.1 - - + -
167A ILE* 1.3 78.1 - - - +
169A ILE* 1.3 67.3 + - - +
170A ASP 3.6 1.4 + - - +
202A SER* 3.3 16.6 - - - +
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Residues in contact with ILE 169 (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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80A LEU* 4.1 3.6 - - - +
97A ILE* 3.7 24.5 - - + +
167A ILE* 3.9 13.0 - - + -
168A ILE* 1.3 75.2 - - - +
170A ASP* 1.3 58.7 + - - +
171A SER* 3.5 28.9 + - - +
182A LEU* 4.8 9.6 - - + +
187A PHE* 3.7 35.2 - - + -
188A TYR* 5.2 1.8 - - + -
191A CYS* 4.3 0.4 - - - -
201A PHE* 3.7 28.7 - - + -
202A SER 2.8 9.9 + - - -
203A ALA* 3.5 11.7 - - + -
204A GLU* 3.2 25.7 + - - +
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Residues in contact with ASP 170 (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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67A MET* 6.2 0.2 - - - +
76A TYR* 2.6 32.3 + - - -
77A HIS* 4.1 9.8 - - - -
80A LEU* 3.7 11.9 - - + -
96A ILE* 4.3 10.3 - - + -
97A ILE 2.7 14.0 + - - +
98A GLY 4.2 0.7 - - - -
99A GLY* 2.9 43.2 + - - +
101A ASP* 5.2 1.0 - - - +
104A THR* 2.7 27.5 + - - +
168A ILE* 3.6 1.2 + - + -
169A ILE* 1.3 70.0 - - - +
171A SER* 1.3 61.4 + - - +
204A GLU* 3.8 1.9 - - - +
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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