Contacts of the strand formed by residues 16 - 25 (chain A) in PDB entry 4FZY
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 3.4 20.6 - - - +
8A GLU 3.7 1.3 - - - +
9A THR* 4.4 2.9 - - + -
15A GLY* 1.3 78.9 - - - +
17A VAL* 1.3 60.5 + - - +
18A GLU 3.4 29.2 - - - +
19A ILE* 4.6 1.1 - - + -
37A VAL* 3.4 23.9 - - + +
39A PRO* 3.3 22.7 - - - +
40A ASP* 4.7 0.6 + - - +
64A ILE* 4.1 34.3 - - + -
88A VAL* 3.6 37.5 - - + +
89A LEU* 3.6 14.4 - - + -
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Residues in contact with VAL 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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8A GLU* 2.9 27.1 + - + +
9A THR 3.9 3.6 - - - +
10A CYS* 4.0 6.7 - - - -
15A GLY 3.9 0.2 + - - -
16A ILE* 1.3 73.9 - - - +
18A GLU* 1.3 60.1 + - - +
36A LEU* 3.6 11.6 - - - +
37A VAL 2.9 29.1 + - - +
39A PRO* 3.1 29.8 - - + -
43A ILE* 3.5 26.9 - - + -
51A HIS* 4.0 12.1 - - + +
53A ILE* 3.8 21.8 - - + -
58A VAL* 3.7 6.9 - - + +
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Residues in contact with GLU 18 (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 THR* 3.4 9.4 + - - -
8A GLU* 3.0 49.7 + - + +
16A ILE* 3.4 6.2 - - - +
17A VAL* 1.3 80.0 - - - +
19A ILE* 1.3 66.3 + - - +
34A SER* 5.2 6.9 + - - -
35A HIS 3.3 15.9 - - - +
36A LEU* 3.9 10.5 + - + +
37A VAL* 4.3 1.6 - - - +
53A ILE* 4.0 2.9 - - + -
131A LEU* 5.0 2.6 - - - +
135A ARG* 2.8 56.2 + - - +
136A ALA* 3.4 16.9 + - + -
137A LEU* 5.0 2.5 + - - +
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Residues in contact with ILE 19 (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 ILE* 4.5 6.1 - - + -
6A ASP 3.5 14.4 - - - +
7A THR* 4.8 2.2 - - - +
16A ILE* 4.6 5.4 - - + -
18A GLU* 1.3 77.7 - - - +
20A ALA* 1.3 66.7 + - - +
34A SER* 3.1 2.8 - - - -
35A HIS* 2.7 41.2 + - + +
37A VAL* 4.2 4.3 - - + -
64A ILE* 4.5 3.6 - - + -
67A VAL* 4.0 17.0 - - + -
68A ILE* 3.8 28.5 - - + -
71A TYR* 3.6 39.0 - - + +
89A LEU* 4.1 23.6 - - + -
136A ALA* 4.0 1.6 - - - -
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Residues in contact with ALA 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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5A ILE* 3.7 1.4 - - - +
6A ASP 3.0 30.8 + - - +
19A ILE* 1.3 81.5 - - - +
21A SER* 1.3 63.5 + - - +
33A MET 3.0 15.3 - - - +
34A SER* 3.4 9.9 - - - -
71A TYR* 3.7 7.1 - - - -
136A ALA* 3.6 4.7 - - + -
137A LEU* 3.3 35.7 - - + +
140A CYS* 3.3 2.8 - - - -
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Residues in contact with SER 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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3A ARG* 3.8 17.6 + - - -
4A ILE 3.0 19.3 - - - -
5A ILE* 4.5 2.2 - - - -
20A ALA* 1.3 76.0 - - - +
22A VAL* 1.3 67.5 + - - +
31A ASN 4.8 0.7 + - - -
33A MET* 2.7 62.4 + - - +
71A TYR* 3.5 12.5 - - - -
137A LEU* 4.0 1.7 - - - +
140A CYS* 3.6 5.2 - - - -
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Residues in contact with VAL 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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3A ARG* 3.5 0.5 - - - +
4A ILE* 2.9 45.9 + - + +
21A SER* 1.3 79.9 - - - +
23A ASP* 1.3 70.2 + - - +
29A ILE* 3.7 22.7 - - + -
30A VAL 3.9 3.4 - - - +
31A ASN 4.0 3.8 - - - -
32A PRO* 3.9 12.3 - - + -
137A LEU* 4.2 4.3 - - + -
140A CYS* 4.1 12.3 - - + +
141A TYR* 3.8 34.5 - - + +
144A ALA* 3.9 15.0 - - + -
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Residues in contact with ASP 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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1A MET* 3.5 27.3 - - + +
2A LEU 3.5 1.8 - - - -
3A ARG* 2.8 38.8 + - - +
21A SER* 4.9 0.3 + - - -
22A VAL* 1.3 79.8 - - - +
24A VAL* 1.3 61.7 + - - +
25A ILE* 4.0 1.8 - - + -
28A LYS 3.4 0.7 - - - +
29A ILE* 3.2 5.4 - - - +
30A VAL* 2.6 54.3 + - + +
31A ASN* 2.9 32.2 + - + +
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Residues in contact with VAL 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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1A MET* 3.9 2.1 - - - -
2A LEU* 2.7 44.2 + - + +
4A ILE* 3.6 24.0 - - + -
22A VAL* 5.2 0.2 - - + -
23A ASP* 1.3 74.1 - - - +
25A ILE* 1.3 63.7 + - - +
26A ASP 4.3 0.6 + - - +
27A GLY* 4.4 10.8 - - - +
28A LYS 3.3 4.7 - - - +
29A ILE* 4.2 6.7 - - + -
144A ALA* 4.1 16.8 - - + -
147A LEU* 4.2 15.5 - - + -
148A ILE* 4.1 30.5 - - + -
151A MET* 5.3 5.6 - - + -
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Residues in contact with ILE 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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1A MET* 3.5 39.3 - - + +
23A ASP* 4.0 2.0 - - + +
24A VAL* 1.3 72.8 - - - +
26A ASP* 1.3 87.9 + - + +
27A GLY 3.3 0.4 - - - -
28A LYS* 2.8 27.7 + - - +
30A VAL* 4.5 21.8 - - + -
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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