Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 4IXU
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A HIS* 1.3 83.5 + - - +
26A VAL* 1.3 63.5 + - - +
64A HIS* 3.2 15.4 - - - +
110A GLY 4.0 15.5 + - - +
111A TYR* 3.4 28.5 - - - -
112A SER* 2.9 26.2 + - - -
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Residues in contact with VAL 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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24A HIS 5.1 1.1 - - - +
25A SER* 1.3 80.6 - - - +
27A ALA* 1.3 67.4 + - - +
28A VAL* 4.2 9.2 - - + -
58A LEU* 4.3 9.0 - - + -
63A CYS* 3.8 26.2 - - + -
64A HIS 2.7 9.1 + - - -
65A LEU* 3.3 17.1 - - + +
66A LYS 2.9 23.0 + - - +
111A TYR* 3.6 3.4 - - - -
112A SER* 3.2 6.3 - - - +
114A VAL* 3.6 30.5 - - + -
323A PHE* 3.7 26.5 - - + -
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Residues in contact with ALA 27 (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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26A VAL* 1.3 74.3 - - - +
28A VAL* 1.3 58.1 + - - +
29A ILE* 4.1 0.4 - - - -
66A LYS 3.2 5.6 - - - +
68A PHE* 3.7 28.5 - - + -
106A ALA* 3.8 11.0 - - + -
111A TYR* 3.7 23.4 - - + +
112A SER 2.7 11.3 + - - +
113A CYS* 4.5 5.6 - - - -
114A VAL* 2.7 35.7 + - - +
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Residues in contact with VAL 28 (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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26A VAL* 4.2 6.3 - - + -
27A ALA* 1.3 79.2 - - - +
29A ILE* 1.3 61.1 + - - +
30A GLY 4.2 0.2 - - - -
50A ARG* 4.0 13.0 - - - +
54A LEU* 4.2 8.3 - - + -
55A MET* 3.7 35.0 - - + -
58A LEU* 4.2 20.6 - - + -
65A LEU* 4.6 3.4 - - + -
66A LYS 2.8 10.7 + - - +
67A ASP* 3.4 5.2 - - - +
68A PHE* 2.8 32.4 + - - +
114A VAL* 3.4 10.3 - - + +
116A LEU* 4.0 28.0 - - + -
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Residues in contact with ILE 29 (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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28A VAL* 1.3 81.2 - - - +
30A GLY* 1.3 67.8 + - - +
31A ALA 3.7 0.3 + - - -
68A PHE* 3.9 19.7 - - + -
69A GLY 3.9 1.8 - - - -
71A LEU* 3.6 34.3 - - + -
99A LEU* 4.0 9.6 - - + -
102A VAL* 3.6 22.7 - - + +
103A VAL* 3.9 17.0 - - + +
106A ALA* 5.0 0.9 - - + -
113A CYS* 3.4 30.7 - - - -
114A VAL 2.8 11.5 + - - +
115A THR* 3.3 5.9 - - + +
116A LEU* 2.8 26.7 + - - +
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Residues in contact with GLY 30 (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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29A ILE* 1.3 72.1 - - - +
31A ALA* 1.3 57.4 + - - -
32A PRO* 3.3 6.7 - - - +
46A PRO* 4.1 9.0 - - - -
50A ARG* 4.0 5.0 - - - +
69A GLY 2.8 18.8 + - - -
70A ASP* 3.5 15.3 - - - -
71A LEU* 2.9 33.8 + - - +
116A LEU* 3.9 7.4 - - - -
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Residues in contact with ALA 31 (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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29A ILE 3.7 0.4 + - - -
30A GLY* 1.3 73.0 - - - +
32A PRO* 1.3 55.0 - - - +
33A PHE* 2.7 29.8 + - + -
46A PRO* 4.0 1.0 - - - +
73A PHE* 4.1 9.2 - - + -
99A LEU* 4.1 13.7 - - + -
115A THR* 3.7 25.1 - - + -
116A LEU 2.8 15.3 + - - +
117A GLY* 3.6 0.9 - - - -
118A GLY* 3.4 14.4 - - - -
122A LEU* 3.7 12.2 - - + +
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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