Contacts of the strand formed by residues 105 - 111 (chain L) in PDB entry 1IJ4
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 THR 105 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2L GLY 5.7 2.1 + - - -
3L ASN 2.9 15.9 + - - -
4L VAL* 3.5 20.0 - - + +
5L ASP 3.0 23.1 + - - -
103L ASP 4.0 0.9 + - - -
104L ALA* 1.3 68.7 - - - +
106L LYS* 1.3 61.6 + - - +
107L VAL* 4.5 9.0 - - + -
129L ILE* 4.3 21.3 - - + -
176L LEU* 5.9 3.4 - - + -
180L ILE* 5.4 7.9 - - + +
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Residues in contact with LYS 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ASP* 3.6 8.1 - - + +
90L ALA* 6.3 0.8 - - - +
94L PHE* 3.7 42.6 + - + +
101L ARG 5.9 5.2 - - - +
104L ALA 3.3 10.6 + - - +
105L THR* 1.3 70.0 - - - +
107L VAL* 1.3 57.9 + - - +
127L ASP* 2.7 43.4 + - - +
128L ILE* 3.7 19.7 - - + +
129L ILE* 2.8 32.1 + - - +
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Residues in contact with VAL 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L VAL* 3.8 27.4 - - + -
5L ASP 2.9 8.2 + - - +
6L LEU* 3.5 32.0 - - + -
7L VAL 2.9 23.8 + - - -
94L PHE* 3.8 6.4 - - - -
105L THR* 3.8 7.2 - - + +
106L LYS* 1.3 76.6 - - - +
108L LEU* 1.3 65.8 + - - +
109L ILE* 5.0 1.3 - - + -
128L ILE* 3.8 2.2 - - - -
129L ILE* 3.6 19.5 - - + +
131L TYR* 4.1 20.0 - - + -
176L LEU* 4.1 20.4 - - + -
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Residues in contact with LEU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L VAL* 3.5 11.9 - - + +
9L LEU* 3.5 34.8 - - + +
86L ILE* 4.1 22.0 - - + +
89L VAL* 3.9 32.1 - - + -
107L VAL* 1.3 75.0 - - - +
109L ILE* 1.3 64.3 + - - +
110L ILE* 4.2 8.1 - - + -
125L ALA* 5.0 2.9 - - + -
128L ILE* 3.5 17.2 - - + +
129L ILE 3.0 9.2 + - - -
130L ARG* 3.4 24.9 - - + -
131L TYR 2.9 27.9 + - - +
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Residues in contact with ILE 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 3.8 28.5 - - + -
7L VAL 3.0 9.8 + - - +
8L PHE* 3.9 15.9 - - + -
9L LEU* 2.9 31.4 + - - +
27L PHE* 4.8 6.1 - - + -
31L VAL* 4.9 0.2 - - + -
107L VAL* 5.0 0.2 - - + -
108L LEU* 1.3 73.3 - - - +
110L ILE* 1.3 61.6 + - - +
111L ILE* 3.5 26.3 - - + +
131L TYR* 3.5 18.4 - - + +
133L ILE* 3.7 31.9 - - + -
173L PHE* 3.7 31.2 - - + -
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Residues in contact with ILE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LEU* 3.5 9.2 - - + +
47L PHE* 4.9 11.2 - - + -
82L THR* 5.0 6.5 - - + -
86L ILE* 3.7 36.6 - - + -
108L LEU* 4.2 13.9 - - + -
109L ILE* 1.3 73.4 - - - +
111L ILE* 1.3 60.3 + - - +
112L THR* 4.1 12.6 + - + -
130L ARG* 4.5 16.6 - - + -
131L TYR 2.9 18.8 + - - +
132L ILE* 3.6 23.4 - - + +
133L ILE 3.1 23.4 + - - +
151L PHE* 4.2 26.5 - - + +
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Residues in contact with ILE 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PHE* 4.5 12.8 - - + -
9L LEU 3.0 24.2 + - - +
10L PHE* 3.6 3.9 - - + -
11L ASP 3.3 24.3 + - - -
24L ILE* 3.7 45.4 - - + +
27L PHE* 4.7 11.4 - - + -
28L MET* 4.6 5.4 - - + -
47L PHE* 4.8 0.2 - - - -
109L ILE* 3.5 39.5 - - + +
110L ILE* 1.3 70.3 - - - +
112L THR* 1.3 60.9 + - - +
133L ILE* 3.3 18.4 - - + +
135L ILE* 4.3 2.5 - - + -
163L LEU* 3.8 18.4 - - + -
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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