Contacts of the strand formed by residues 1 - 12 (chain A) in PDB entry 1IFC
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 ALA 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE* 1.4 67.2 + - + +
3A ASP* 3.5 21.4 + - - +
6A TRP* 3.8 9.0 - - - -
108A ILE* 3.7 26.9 - - - +
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Residues in contact with PHE 2 (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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1A ALA* 1.4 77.9 - - + +
3A ASP* 1.3 67.1 + - - +
4A GLY 3.5 1.2 + - - -
6A TRP* 3.0 21.3 + + - -
40A ILE* 3.5 32.3 - - + +
47A PHE* 4.7 9.0 - + + -
84A MET* 4.2 19.1 - - + -
87A ASN 3.6 22.2 - - - -
89A LEU* 4.1 30.7 - - + -
106A ARG* 3.3 32.5 - - + -
107A GLU* 4.3 2.5 - - - -
108A ILE* 3.8 21.8 - - + -
113A LEU* 3.7 23.8 - - + -
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Residues in contact with ASP 3 (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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1A ALA* 3.5 26.6 + - - +
2A PHE* 1.3 77.4 + - - +
4A GLY* 1.3 53.3 + - - +
6A TRP* 4.5 0.5 - - - -
40A ILE* 3.7 10.5 - - - +
41A THR* 5.1 0.7 - - - -
42A GLN* 4.5 25.6 + - - +
47A PHE* 5.9 0.9 - - - -
130A LYS* 2.5 25.6 + - - -
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Residues in contact with GLY 4 (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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3A ASP* 1.3 76.6 - - - +
5A THR* 1.3 62.1 - - - -
6A TRP* 3.5 6.9 - - - -
39A THR* 3.5 3.6 - - - -
40A ILE 2.9 35.9 + - - -
41A THR* 5.7 0.4 - - - +
130A LYS* 2.9 12.1 - - - -
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Residues in contact with THR 5 (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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4A GLY* 1.3 73.1 - - - -
6A TRP* 1.3 65.0 + - - +
7A LYS* 5.9 0.7 - - + -
37A LYS* 3.7 32.5 - - + -
38A LEU 3.3 3.4 - - - +
39A THR* 3.3 24.4 + - - +
130A LYS* 3.0 11.0 - - - +
131A GLU* 2.9 46.5 + - - +
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Residues in contact with TRP 6 (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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1A ALA 3.8 18.8 - - - -
2A PHE* 3.0 18.8 + - - -
4A GLY 3.5 12.5 + - - -
5A THR* 1.3 75.3 - - - +
7A LYS* 1.3 59.5 + - - +
37A LYS* 3.3 5.4 - - - +
38A LEU* 2.8 39.8 + - + +
40A ILE* 4.1 15.9 - - + +
108A ILE* 4.0 22.9 - - + -
111A ASN* 3.5 25.6 - - - -
112A GLU 4.4 1.3 - - - -
113A LEU* 3.5 34.1 - - + -
128A PHE* 3.8 19.3 - - + -
129A LYS 3.4 8.3 - - - -
130A LYS* 2.8 56.5 - - + +
131A GLU 5.1 0.2 - - - -
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Residues in contact with LYS 7 (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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5A THR* 5.9 0.2 - - + -
6A TRP* 1.3 74.3 - - - +
8A VAL* 1.3 77.2 + - - +
9A ASP* 4.2 0.7 - - - -
35A ASN* 3.4 35.9 + - - +
36A LEU 3.1 25.6 - - - +
37A LYS* 3.9 29.4 - - + +
128A PHE* 3.7 2.9 - - - -
129A LYS* 2.9 32.6 + - + +
131A GLU 4.9 12.1 - - - +
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS* 1.3 82.5 - - + +
9A ASP* 1.3 61.8 + - - +
10A ARG 4.2 5.4 - - - +
11A ASN* 3.7 22.9 - - - +
34A ASP* 4.2 1.3 - - - +
35A ASN* 4.2 6.5 - - - +
36A LEU* 2.9 40.5 + - + +
126A ARG* 3.8 30.3 - - + +
127A ILE 3.8 8.3 - - - +
128A PHE* 3.4 19.3 - - + -
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Residues in contact with ASP 9 (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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7A LYS 3.3 1.5 + - - +
8A VAL* 1.3 75.3 - - - +
10A ARG* 1.3 92.9 + - - +
127A ILE 2.8 16.7 + - - +
129A LYS* 3.3 41.8 - - + +
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Residues in contact with ARG 10 (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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8A VAL* 3.9 1.2 - - - +
9A ASP* 1.3 110.7 + - - +
11A ASN* 1.3 74.7 + - - +
12A GLU* 5.1 6.5 + - + -
112A GLU* 2.7 43.8 + - - -
127A ILE* 2.9 63.7 + - + +
129A LYS* 3.6 2.8 - - - +
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Residues in contact with ASN 11 (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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8A VAL* 3.7 4.2 - - - +
10A ARG* 1.3 85.1 - - - +
12A GLU* 1.3 69.2 + - - +
13A ASN 4.3 0.4 + - - -
14A TYR* 3.8 17.5 - - + +
32A ALA* 3.2 38.0 + - - +
125A LYS 3.3 9.4 - - - +
126A ARG* 2.8 35.4 + - - +
127A ILE* 5.7 0.2 - - - -
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Residues in contact with GLU 12 (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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10A ARG* 5.1 6.6 + - + -
11A ASN* 1.3 79.6 - - - +
13A ASN* 1.3 70.1 + - + +
14A TYR 3.0 1.7 + - - -
124A ALA* 3.3 0.9 - - - -
125A LYS* 2.9 56.2 + - + +
127A ILE* 4.1 23.9 - - + +
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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