Contacts of the strand formed by residues 4 - 11 (chain A) in PDB entry 3K47
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 LEU 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL 5.6 1.6 - - - +
2A ARG* 3.4 11.0 + - - +
3A PRO* 1.3 76.1 - - - +
5A ASN* 1.3 62.1 + - - +
93A LEU* 5.2 0.2 - - + -
97A LEU* 3.8 36.8 - - + -
112A VAL* 4.2 15.3 - - + -
114A ILE* 4.6 16.6 - - + -
124A ALA* 4.5 8.7 - - + +
127A GLN* 3.9 28.9 - - + -
130A HIS 3.0 8.9 + - - +
131A LEU* 3.2 31.0 - - + +
132A ARG 2.9 25.1 + - - -
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Residues in contact with ASN 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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3A PRO* 3.9 10.3 + - - +
4A LEU* 1.3 73.0 - - - +
6A CYS* 1.3 56.0 + - - +
111A MET* 3.9 23.0 - - - +
112A VAL 2.9 31.1 + - - +
113A TRP* 3.1 28.7 - - + -
114A ILE* 2.6 32.5 + - - -
132A ARG* 2.8 44.2 + - - +
134A PHE* 3.7 8.4 - - + -
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Residues in contact with CYS 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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5A ASN* 1.3 74.1 - - - +
7A ILE* 1.3 54.3 + - - +
8A VAL* 5.6 1.3 - - + -
114A ILE* 3.5 18.2 - - - -
121A TYR* 4.1 19.1 - - + -
124A ALA* 3.8 28.5 - - - -
125A MET* 4.8 5.4 - - - -
131A LEU* 3.9 15.9 - - - -
132A ARG 2.9 6.1 + - - +
133A LEU* 3.8 21.3 - - + -
134A PHE* 2.7 35.3 + - - +
148A PHE* 5.3 4.7 - - + -
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Residues in contact with ILE 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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6A CYS* 1.3 74.3 - - - +
8A VAL* 1.3 58.1 + - - +
33A TYR* 4.1 21.3 - - + -
34A PHE* 3.9 26.5 - - + +
37A MET* 4.2 13.7 - - + -
38A THR* 3.9 1.8 - - + -
113A TRP* 3.8 26.7 - - + -
114A ILE 3.2 5.2 + - - +
115A VAL* 3.7 28.3 - - + -
121A TYR* 2.6 26.4 + - - -
134A PHE* 3.3 22.2 - - + +
188A D09 3.2 19.8 - - - +
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Residues in contact with VAL 8 (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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6A CYS 5.6 1.6 - - - -
7A ILE* 1.3 76.8 - - - +
9A ALA* 1.3 63.4 + - - +
10A VAL* 3.5 27.6 - - + -
16A ILE* 3.7 10.3 - - + -
121A TYR* 3.5 28.7 - - + +
133A LEU* 6.3 0.2 - - + -
134A PHE 3.1 6.1 + - - +
135A VAL* 4.0 17.9 - - + -
136A THR 2.9 21.0 + - - -
148A PHE* 3.6 27.1 - - + -
187A NDP 3.5 9.4 - - - +
188A D09 3.0 17.4 + - - -
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Residues in contact with ALA 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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8A VAL* 1.3 71.9 - - - +
10A VAL* 1.3 65.4 + - - +
16A ILE* 3.7 0.7 - - - +
22A LEU* 6.3 0.2 - - + -
24A TRP* 3.4 23.8 - - + +
27A LEU* 6.1 0.2 - - + -
30A GLU* 4.2 9.6 - - + +
136A THR* 3.6 24.0 - - + +
138A ILE* 4.4 6.1 - - + -
187A NDP 2.9 32.3 + - - +
188A D09 3.3 13.4 + - + +
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Residues in contact with VAL 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* 3.5 29.6 - - + -
9A ALA* 1.3 82.9 - - - +
11A SER* 1.3 70.7 + - - +
14A MET* 4.8 7.2 - - - -
15A GLY 3.4 4.7 - - - +
16A ILE* 3.7 10.8 - - + -
24A TRP* 4.1 2.4 - - - -
135A VAL* 3.4 25.6 - - + -
136A THR 2.8 13.5 + - - +
137A ARG* 3.8 20.6 - - - +
138A ILE* 2.9 27.4 + - - +
148A PHE* 3.8 17.7 - - + -
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Residues in contact with SER 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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10A VAL* 1.3 80.7 - - - +
12A GLN* 1.3 61.9 + - - +
13A ASN* 3.1 14.0 + - - -
14A MET* 2.9 21.1 + - - +
15A GLY* 2.7 42.2 + - - -
24A TRP* 3.4 21.1 - - - -
137A ARG* 5.7 0.2 + - - -
138A ILE* 3.6 7.2 - - - -
140A GLN 3.4 11.9 - - - -
142A PHE* 4.0 11.6 + - - -
144A SER* 4.0 2.8 + - - -
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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