Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 4FUB
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.4 8.5 - - - +
43A SER 2.8 31.8 + - - +
44A ALA 3.9 5.8 - - - -
45A THR* 3.7 19.5 - - - +
48A PHE* 4.1 13.0 - - + -
82A ILE 3.3 12.6 - - - +
83A LEU* 3.9 12.6 - - + -
98A ILE* 1.3 76.2 - - - +
100A LEU* 1.3 63.3 + - - +
101A LEU* 4.5 4.5 - - + -
240A TRP* 4.2 2.7 - - - -
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Residues in contact with LEU 100 (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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36A ILE* 3.9 28.5 - - + -
40A TRP* 3.7 16.8 - - + -
41A VAL 3.5 5.6 - - - +
42A ILE* 3.9 20.0 - - + -
80A ASN 3.6 1.9 - - - +
81A LEU* 3.7 1.7 - - - -
82A ILE* 2.9 40.1 + - + +
99A ALA* 1.3 75.2 - - - +
101A LEU* 1.3 63.6 + - - +
102A LYS 4.1 0.4 - - - -
240A TRP* 3.6 27.3 - - + -
241A ILE* 4.4 5.2 - - + +
244A HIS* 3.7 28.5 - - + +
245A THR* 3.8 20.9 - - + -
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Residues in contact with LEU 101 (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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18A ILE* 4.3 10.1 - - + -
40A TRP* 3.7 2.4 - - - -
41A VAL* 2.8 48.0 + - + +
43A SER* 4.3 11.2 - - - -
48A PHE* 3.9 36.1 - - + -
57A TYR* 5.1 2.2 - - + -
59A VAL* 4.0 14.6 - - + -
78A VAL* 3.7 30.1 - - + -
80A ASN 3.5 3.8 - - - -
81A LEU* 3.8 23.3 - - + -
99A ALA* 4.5 0.4 - - + -
100A LEU* 1.3 82.1 - - - +
102A LYS* 1.4 63.8 + - - +
103A ILE* 3.4 6.1 + - + +
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Residues in contact with LYS 102 (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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39A CYS* 3.2 26.9 - - + +
40A TRP* 3.6 34.0 - - + +
78A VAL* 3.5 4.3 - - - -
79A GLU* 2.7 66.8 + - + +
80A ASN* 2.9 25.9 + - + +
101A LEU* 1.4 70.3 - - - +
103A ILE* 1.3 57.6 + - - +
110A CYS* 5.5 2.0 - - - -
309A 15P 3.1 39.5 - - + +
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Residues in contact with ILE 103 (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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35A LEU* 3.9 9.0 - - + -
38A PRO 3.6 18.2 - - - +
39A CYS* 2.9 24.8 + - - +
40A TRP 4.3 0.7 - - - +
41A VAL* 4.0 10.1 - - + -
59A VAL* 4.0 34.8 - - + -
61A LEU* 3.7 29.6 - - + -
76A PHE* 3.9 22.7 - - + -
77A GLU 3.5 7.4 - - - +
78A VAL* 5.1 0.7 - - + -
79A GLU* 4.5 3.6 - - - +
101A LEU* 4.0 11.4 - - + +
102A LYS* 1.3 77.1 - - - +
104A ARG* 1.3 64.5 + - - +
110A CYS* 4.0 18.4 - - - -
111A ALA 5.0 0.4 - - - +
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Residues in contact with ARG 104 (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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54A LYS* 4.8 11.3 - - - +
76A PHE* 3.7 5.6 - - - +
77A GLU* 2.9 43.3 + - + +
78A VAL 5.0 1.8 + - - -
79A GLU* 3.7 56.3 + - + +
103A ILE* 1.3 76.5 - - - +
105A SER* 1.3 70.2 + - - +
108A GLY* 4.4 17.5 - - - +
109A ARG 3.4 9.0 - - - +
110A CYS* 5.9 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