Contacts of the strand formed by residues 11 - 17 (chain A) in PDB entry 4KAL
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 ILE 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 3.3 13.4 + - + +
10A ALA* 1.3 78.9 - - - +
12A VAL* 1.3 71.6 + - - +
13A ASP* 3.7 2.2 - - - +
56A GLY 2.8 30.8 + - - -
57A GLY* 3.9 8.2 - - - +
88A PHE* 3.4 12.5 - - - -
110A THR* 5.4 0.2 - - - -
111A ALA* 3.6 16.6 - - + -
112A ARG* 3.8 4.3 - - - -
113A SER* 3.6 19.1 - - - +
127A THR* 3.8 11.4 - - + -
129A LEU* 4.8 0.7 - - + -
401A ADN 3.3 66.9 - - + +
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Residues in contact with VAL 12 (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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11A ILE* 1.3 75.7 - - - +
13A ASP* 1.3 73.8 + - - +
14A ILE* 4.4 2.2 - - + +
53A GLU* 4.3 12.1 - - + -
54A ALA 3.8 13.7 - - - +
55A SER* 4.6 2.2 - - - +
56A GLY 4.2 0.2 - - - +
84A LEU* 3.5 53.6 - - + +
87A ILE* 4.6 10.8 - - + -
88A PHE* 4.2 16.4 - - + +
110A THR* 4.5 4.0 - - + -
111A ALA 3.1 10.1 + - - +
112A ARG* 3.1 11.8 - - + +
113A SER 3.0 20.6 + - - -
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Residues in contact with ASP 13 (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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11A ILE* 3.7 4.3 - - - +
12A VAL* 1.3 76.3 - - - +
14A ILE* 1.3 60.4 + - - +
15A ILE* 3.9 20.1 - - + +
53A GLU* 3.2 10.0 - - - +
54A ALA* 2.7 40.5 + - + +
56A GLY* 3.6 3.3 - - - -
113A SER* 3.5 5.1 - - - -
115A ILE* 3.5 16.8 - - + +
312A PRO* 3.4 16.5 - - - +
401A ADN 2.4 50.5 + - - -
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Residues in contact with ILE 14 (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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12A VAL* 4.4 7.0 - - + +
13A ASP* 1.3 76.8 - - - +
15A ILE* 1.3 55.8 + - - +
45A TYR* 3.8 15.3 - - + +
48A MSE 3.2 20.9 - - - +
51A ALA* 3.6 22.9 - - + -
52A LEU 3.6 3.4 - - - -
53A GLU* 3.8 19.7 - - + +
84A LEU* 5.7 5.8 - - + -
112A ARG* 3.9 18.4 - - + -
113A SER 2.9 12.7 + - - +
114A MSE 4.0 7.2 - - + -
115A ILE 2.8 30.3 + - - -
403A DMS 3.6 31.6 - - + -
87B ILE* 5.8 4.0 - - + -
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Residues in contact with ILE 15 (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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13A ASP* 3.9 23.8 - - + +
14A ILE* 1.3 77.8 - - - +
16A SER* 1.3 63.9 + - - +
17A ARG* 3.5 10.7 + - - +
51A ALA* 3.2 5.8 - - - -
52A LEU* 2.9 58.4 + - + +
54A ALA* 4.3 7.9 - - + -
115A ILE* 3.4 19.5 - - + +
117A VAL* 4.1 20.4 - - + -
270A ASP* 4.8 3.8 - - - +
272A THR* 6.0 1.8 - - + +
310A ILE* 4.2 17.0 - - + -
311A GLY* 4.0 24.2 - - - +
312A PRO* 4.3 2.7 - - + -
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Residues in contact with SER 16 (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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15A ILE* 1.3 76.7 - - - +
17A ARG* 1.3 86.2 + - - +
48A MSE 3.7 29.1 - - - +
49A GLY* 3.8 13.9 + - - -
50A PRO 3.1 20.7 + - - -
51A ALA* 4.4 0.4 - - - -
115A ILE 3.0 8.8 + - - +
116A PHE* 3.4 6.5 - - - -
117A VAL* 2.9 24.5 + - - +
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Residues in contact with ARG 17 (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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15A ILE* 3.5 27.5 + - - +
16A SER* 1.3 90.5 + - - +
18A CYS* 1.3 63.4 + - - +
49A GLY* 5.6 1.9 + - - -
50A PRO 3.7 16.2 + - - -
51A ALA* 4.3 4.0 - - - +
52A LEU* 4.2 7.1 - - - +
116A PHE* 5.1 0.5 - - - -
117A VAL* 3.3 19.2 - - + +
310A ILE* 4.1 27.4 - - + +
315B MSE 4.0 55.5 + - - +
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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