Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 2INU
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 GLY 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PRO 3.1 3.2 + - - -
104A PRO* 1.3 76.2 - - - +
106A ASP* 1.3 64.4 + - - -
107A TYR* 3.6 13.4 - - - -
150A ALA 2.9 10.6 + - - +
152A HIS* 3.0 31.7 + - - +
53C ASN* 4.2 2.2 - - - -
96C PRO* 3.6 15.3 - - - +
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Residues in contact with ASP 106 (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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71A GLN* 4.1 17.8 - - - +
105A GLY* 1.3 71.0 - - - -
107A TYR* 1.3 67.5 - - - +
147A GLN* 5.6 4.3 - - - +
148A PRO 4.1 3.8 - - - +
152A HIS* 2.9 30.9 - - + +
154A ARG* 5.6 4.0 - - - -
93C ASP 4.0 6.1 - - - +
94C ALA* 3.7 17.3 - - - +
95C ARG 4.3 0.3 + - - -
96C PRO* 3.0 34.2 - - + +
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Residues in contact with TYR 107 (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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57A VAL* 4.6 2.0 - - + -
58A THR* 3.5 15.7 - - + +
70A ALA* 3.3 43.3 - - + +
71A GLN* 3.9 9.4 - - + -
74A ILE* 4.1 17.7 - - + -
102A ILE* 3.4 23.6 - - + -
103A PRO* 2.6 45.9 + - - +
104A PRO 3.7 4.9 + - - -
105A GLY* 3.6 17.5 - - - -
106A ASP* 1.3 77.9 - - - +
108A ASP* 1.3 58.9 + - - +
151A SER* 4.6 0.9 - - - -
152A HIS 2.8 23.5 + - - +
153A ILE* 3.4 3.5 - - + -
154A ARG* 2.7 36.5 + - - +
52C PRO* 5.4 0.9 - - - +
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Residues in contact with ASP 108 (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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70A ALA 3.8 0.2 + - - -
71A GLN 3.2 21.8 + - - +
72A SER* 3.5 12.3 - - - +
73A ASP* 3.1 6.8 - - - -
74A ILE* 2.9 24.6 + - - -
107A TYR* 1.3 73.5 - - - +
109A LEU* 1.3 60.4 + - - +
110A HIS* 3.9 7.0 + - + -
154A ARG* 3.2 35.5 + - - -
156A LEU* 3.7 21.6 - - + +
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Residues in contact with LEU 109 (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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73A ASP* 4.0 1.8 - - - -
74A ILE* 3.9 11.0 - - + -
75A GLY* 3.8 13.0 - - - -
108A ASP* 1.3 72.8 - - - +
110A HIS* 1.3 58.0 + - - +
111A THR 3.3 28.5 - - - +
113A VAL* 4.3 1.1 - - + -
153A ILE* 3.8 24.9 - - + -
154A ARG 2.7 16.9 + - - +
155A VAL* 4.4 2.9 - - - -
156A LEU* 2.7 32.5 + - - +
157A THR* 3.8 19.5 - - + -
164A ALA* 4.1 31.6 - - + +
165A PHE* 4.3 14.1 - - + -
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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