Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 4F80
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 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.8 4.5 - - + -
13A ALA* 3.9 17.7 - - + -
18A ASP* 1.3 75.7 - - - +
20A ASP* 1.3 64.0 + - - +
21A LEU* 4.0 2.3 + - + +
82A LEU 3.4 2.4 - - - +
83A ARG* 3.2 1.7 - - - -
84A ILE* 2.8 38.1 + - + +
87A VAL* 3.6 21.1 - - + +
112A LEU* 3.9 20.6 - - + -
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Residues in contact with ASP 20 (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 20.2 - - - +
18A ASP* 5.2 1.3 - - - +
19A ALA* 1.3 73.6 + - - +
21A LEU* 1.3 62.0 + - - +
22A PRO* 3.3 11.6 - - + +
71A LEU* 3.7 11.9 - - - +
81A ALA* 4.7 9.0 - - + -
82A LEU 3.4 3.4 - - - +
83A ARG* 2.8 55.5 + - - +
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Residues in contact with LEU 21 (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* 3.6 33.0 - - + -
19A ALA* 4.8 1.8 - - + +
20A ASP* 1.3 76.1 - - - +
22A PRO* 1.3 62.4 - - - +
38A TRP* 3.8 15.9 + - + +
81A ALA* 3.2 2.0 - - - -
82A LEU* 2.7 49.0 + - + +
84A ILE* 4.1 21.8 - - + -
95A TYR* 3.7 37.9 - - + -
110A VAL* 3.9 17.5 - - + -
111A GLU 4.4 0.4 - - - +
112A LEU* 3.9 19.5 - - + -
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Residues in contact with PRO 22 (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 GLY 4.0 0.2 - - - -
7A PRO* 3.2 41.9 - - + +
11A ILE* 4.0 15.0 - - + -
20A ASP* 3.3 12.6 - - + +
21A LEU* 1.3 86.8 - - - +
23A CYS* 1.3 67.4 + - - +
24A HIS* 5.6 0.9 - - - -
80A ALA 3.5 9.9 - - - +
81A ALA* 3.8 9.9 - - + -
110A VAL* 3.6 1.1 - - + +
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Residues in contact with CYS 23 (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 VAL* 4.1 0.7 - - + -
5A LEU 3.3 11.4 - - - +
6A GLY* 4.4 0.9 - - - -
21A LEU 4.2 0.4 + - - -
22A PRO* 1.3 73.5 - - - +
24A HIS* 1.3 65.7 + - - +
38A TRP* 4.4 4.9 - - + -
79A LYS* 3.8 0.9 - - - +
80A ALA 2.9 32.5 + - - +
97A CYS* 1.9 55.6 - - + -
99A PHE* 3.8 15.8 - - + -
110A VAL* 3.3 26.9 - - - -
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Residues in contact with HIS 24 (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 VAL* 3.6 2.4 - - - -
5A LEU* 2.9 72.3 + - + +
6A GLY 3.9 11.9 + - - -
7A PRO* 5.7 0.9 - - + -
22A PRO 5.5 0.8 + - - -
23A CYS* 1.3 78.1 - - - +
25A LEU* 1.3 76.2 + - - +
26A PHE* 5.3 1.1 - + + -
28A THR* 5.9 1.6 - - - -
77A ALA 5.7 0.4 - - - +
78A GLY 3.2 10.3 - - - +
79A LYS* 4.0 20.6 - - + -
99A PHE* 4.4 3.3 - - - -
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Residues in contact with LEU 25 (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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2A PHE* 3.5 31.2 - - + -
3A SER 3.4 1.6 - - - -
4A VAL* 4.0 5.4 - - + -
24A HIS* 1.3 87.4 - - - +
26A PHE* 1.3 59.8 + - - +
27A PRO 3.8 16.3 - - - +
28A THR* 3.8 8.0 + - - -
29A MET* 3.7 31.6 - - + +
30A SER 4.1 0.2 - - - +
31A ALA* 3.8 15.7 - - + -
34A MET* 3.7 23.6 - - + -
77A ALA 5.0 1.2 - - - +
78A GLY* 2.9 21.4 + - - +
99A PHE* 3.4 30.1 - - + -
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Residues in contact with PHE 26 (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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2A PHE* 3.4 4.8 - - - -
3A SER* 2.7 52.9 + - - +
5A LEU* 3.8 31.6 - - + -
24A HIS* 6.0 0.9 - + - -
25A LEU* 1.3 74.9 - - - +
27A PRO* 1.3 87.2 - - + +
28A THR 5.1 0.7 - - - -
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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