Contacts of the strand formed by residues 4 - 11 (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 VAL 4 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L GLY 4.3 4.9 - - - +
3L ASN* 1.3 79.5 - - - +
5L ASP* 1.3 62.0 + - - +
6L LEU 4.2 0.4 - - - +
39L SER* 3.4 12.7 + - - +
40L TYR* 3.4 49.4 - - + +
41L GLN 3.2 13.0 + - - +
101L ARG* 3.1 13.9 + - - +
105L THR* 3.5 26.9 - - + +
107L VAL* 3.8 19.7 - - + -
176L LEU* 4.6 11.2 - - + +
180L ILE* 4.7 12.3 - - + -
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Residues in contact with ASP 5 (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* 1.3 69.6 - - - +
6L LEU* 1.3 60.1 + - - +
41L GLN* 3.6 15.0 - - - +
57L PHE* 3.9 8.7 - - + -
94L PHE* 3.4 25.0 - - + -
99L GLY 4.2 0.2 - - - +
100L ALA* 3.5 9.2 - - - -
101L ARG* 2.7 66.4 + - - +
104L ALA* 3.1 18.5 - - + +
105L THR 3.0 10.4 + - - +
106L LYS* 3.6 2.0 - - + -
107L VAL* 2.9 23.6 + - - -
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Residues in contact with LEU 6 (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* 4.2 0.4 - - + -
5L ASP* 1.3 72.2 - - - +
7L VAL* 1.3 73.5 + - - +
8L PHE* 3.9 12.6 - - + -
40L TYR* 4.5 14.4 - - + -
41L GLN 2.9 10.0 + - - +
42L PHE* 3.4 36.1 - - + -
43L ALA 3.1 22.9 + - - +
57L PHE* 3.7 0.9 - - - -
107L VAL* 3.5 35.7 - - + +
109L ILE* 3.8 22.4 - - + -
173L PHE* 4.0 26.2 - - + -
176L LEU* 4.3 5.2 - - + -
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Residues in contact with VAL 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LEU* 1.3 74.6 - - - +
8L PHE* 1.3 65.6 + - - +
9L LEU 3.6 1.4 + - - +
43L ALA* 3.5 10.3 - - + +
45L VAL* 4.1 19.1 - - + -
57L PHE* 3.5 26.2 - - + -
89L VAL* 3.8 32.3 - - + -
93L VAL* 3.6 19.3 - - + -
94L PHE* 3.6 19.1 - - + -
107L VAL 2.9 12.4 + - - +
108L LEU* 3.5 4.2 - - + +
109L ILE 3.0 25.5 + - - -
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Residues in contact with PHE 8 (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* 3.9 7.6 - - + -
7L VAL* 1.3 71.3 - - - +
9L LEU* 1.3 58.3 + - - +
10L PHE* 3.5 4.0 - - - -
27L PHE* 5.7 2.0 - + - -
28L MET* 3.6 52.7 - - + -
31L VAL* 3.7 33.2 - - + -
32L MET* 3.7 26.7 - - + -
42L PHE* 3.5 29.2 - + + -
43L ALA 2.9 22.8 + - - +
44L ALA* 4.6 3.8 - - + -
45L VAL 2.9 28.7 + - - +
55L PHE* 5.1 1.8 - + - -
70L LEU* 6.2 0.2 - - + -
109L ILE* 3.9 23.1 - - + -
111L ILE* 4.5 6.5 - - + -
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Residues in contact with LEU 9 (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 3.6 1.6 + - - -
8L PHE* 1.3 69.7 - - - +
10L PHE* 1.3 58.3 + - - +
45L VAL* 3.5 34.1 - - + +
47L PHE* 3.7 29.6 - - + -
85L ALA* 3.8 24.5 - - + +
86L ILE* 3.6 31.4 - - + -
89L VAL* 3.9 16.4 - - + -
108L LEU* 3.5 22.2 - - + -
109L ILE 2.9 12.0 + - - +
110L ILE* 3.5 7.6 - - + -
111L ILE* 3.0 26.3 + - - +
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Residues in contact with PHE 10 (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 3.5 5.8 - - - -
9L LEU* 1.3 74.0 - - - +
11L ASP* 1.3 61.7 + - - +
12L GLY 3.6 0.2 + - - -
21L PHE* 4.0 24.9 - + - -
24L ILE* 3.6 26.5 - - + -
28L MET* 3.3 35.4 - - + -
44L ALA* 4.2 9.6 - - + -
45L VAL 2.9 38.9 + - - -
46L GLN* 3.4 30.7 - - + -
47L PHE* 2.9 29.1 + - - -
54L GLU* 4.0 8.7 - - + -
70L LEU* 5.2 0.9 - - + -
73L VAL* 3.8 30.3 - - + -
111L ILE* 3.6 5.8 - - + +
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Residues in contact with ASP 11 (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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1L MG 4.0 1.6 - - - -
10L PHE* 1.3 71.9 - - - +
12L GLY* 1.3 57.1 + - - +
13L SER* 2.5 43.0 + - - -
16L LEU* 3.3 21.5 - - + +
21L PHE* 3.4 22.4 - - - -
24L ILE* 4.6 1.2 - - - +
47L PHE* 3.4 27.5 - - + +
80L THR* 3.2 20.8 - - - +
111L ILE 3.3 6.9 + - - +
112L THR* 2.5 33.7 + - - +
114L GLY 3.9 0.9 - - - +
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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