Contacts of the strand formed by residues 100 - 106 (chain A) in PDB entry 5FSJ
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLY 3.0 7.2 + - - +
39A ILE* 3.3 21.3 - - + +
40A PHE* 2.8 28.4 + - - +
77A ALA* 4.3 13.2 - - + +
81A TYR* 4.0 21.8 - - + -
92A SER* 3.5 25.6 - - - +
93A TYR* 3.9 12.3 - - + -
98A ALA 3.8 0.9 - - - +
99A ALA* 1.3 72.9 - - - +
101A ARG* 1.3 61.7 + - - +
102A SER* 4.3 0.8 + - - +
115A TRP* 6.1 1.1 - - + -
120A MET* 3.5 32.1 - - + -
144A LEU* 4.1 13.0 - - + -
1008A OXY 3.6 16.6 - - - +
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Residues in contact with ARG 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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40A PHE* 3.3 31.2 - - + -
42A TYR* 2.8 45.4 + - + -
51A PRO* 5.8 4.0 - - - -
93A TYR* 5.5 0.4 - - - -
99A ALA* 3.6 30.1 + - - +
100A ILE* 1.3 79.1 - - - +
102A SER* 1.3 63.2 + - - +
115A TRP* 4.9 1.7 - - - -
118A SER 4.9 6.8 + - - +
119A GLN* 3.3 22.6 - - + +
120A MET* 2.9 26.5 + - - +
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Residues in contact with SER 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 ILE* 5.7 1.0 - - - +
40A PHE 3.0 9.7 + - - -
41A THR* 3.3 8.7 + - - +
42A TYR* 2.8 35.0 + - - -
73A ALA* 4.3 20.2 + - - -
77A ALA* 4.7 3.3 - - - +
100A ILE* 4.8 1.2 + - - +
101A ARG* 1.3 72.5 - - - +
103A SER* 1.3 56.8 + - - +
119A GLN* 4.0 1.1 - - - -
120A MET* 3.2 33.3 - - - +
122A TYR* 4.0 20.3 - - - -
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Residues in contact with SER 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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42A TYR* 3.4 8.2 - - - +
44A ALA* 4.4 7.4 - - - -
50A LEU* 3.9 15.0 - - - -
51A PRO* 2.6 31.9 + - - +
102A SER* 1.3 73.8 - - - +
104A VAL* 1.3 62.0 + - - +
106A TYR* 5.5 0.2 - - - -
119A GLN* 2.8 24.6 + - - -
120A MET 2.9 7.8 + - - -
121A VAL* 3.5 5.1 - - - +
122A TYR* 2.9 29.7 + - - +
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Residues in contact with VAL 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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41A THR* 4.6 3.6 - - + -
42A TYR 3.0 16.4 + - - +
44A ALA* 2.9 27.0 + - - +
55A TRP* 3.7 25.6 - - + -
69A PRO* 3.6 28.7 - - + +
70A ALA* 3.9 16.4 - - + +
73A ALA* 3.6 20.2 - - + -
103A SER* 1.3 77.7 - - - +
105A HIS* 1.3 70.9 + - + +
106A TYR 3.2 2.6 + - - -
122A TYR* 3.7 17.0 - - + +
134A SER* 4.4 1.6 - - - +
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Residues in contact with HIS 105 (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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43A ASP* 3.7 13.2 - - - +
44A ALA* 3.6 1.2 - - - +
45A LYS 3.6 5.6 + - - +
46A TYR* 2.8 36.6 + + + +
55A TRP* 3.9 10.7 - + - -
65A SER 5.3 0.2 - - - -
66A TYR* 2.7 73.3 + + - +
69A PRO* 3.9 16.3 - - + +
104A VAL* 1.3 80.2 - - + +
106A TYR* 1.3 59.9 + - - +
107A SER 3.4 2.4 + - - -
122A TYR 3.5 4.6 + - - -
124A ASP* 2.8 44.8 + - - +
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Residues in contact with TYR 106 (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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44A ALA* 4.0 5.2 - - + -
47A ARG 3.7 11.0 - - - -
48A THR* 3.6 39.5 + - + +
50A LEU* 3.9 20.5 - - + +
103A SER 5.0 0.4 - - - +
104A VAL 3.2 2.5 - - - -
105A HIS* 1.3 71.9 - - - +
107A SER* 1.3 79.5 + - - +
110A TYR* 3.4 45.1 + + - +
114A PHE* 3.8 24.4 - + - -
121A VAL* 3.3 29.4 - - + -
122A TYR 3.2 17.3 + - - +
123A GLY* 3.8 4.9 - - - -
124A ASP 4.5 1.6 + - - -
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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