Contacts of the strand formed by residues 103 - 108 (chain D) in PDB entry 1SZU
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 LYS 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLN 4.1 5.9 - - - +
94D ASN* 2.7 53.9 + - - +
95D GLN* 4.3 5.3 + - - +
97D VAL* 2.9 28.8 + - + +
98D PRO 3.4 13.5 - - - +
99D GLY* 2.9 30.7 + - - -
101D PHE* 3.5 19.0 + - + +
102D ALA* 1.3 81.1 - - - +
104D LYS* 1.3 68.5 + - - +
280D THR* 3.8 17.5 - - + -
281D GLY* 3.2 17.3 - - - +
283D ALA* 3.7 3.3 - - - +
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 2.8 30.7 + - - +
13C GLN* 3.9 11.9 - - - +
14C ALA 3.3 12.3 - - - +
15C ILE 2.8 24.8 + - - +
16C PRO* 3.9 5.6 - - + +
17C ARG* 4.1 4.0 - - - +
94D ASN* 2.9 7.0 - - - -
103D LYS* 1.3 78.3 - - - +
105D THR* 1.3 59.5 + - - +
280D THR* 3.3 1.9 - - - -
281D GLY 3.0 29.3 + - - +
283D ALA* 3.9 15.5 - - + +
286D MET* 3.4 22.1 - - + +
287D ASP* 2.8 41.7 + - - +
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ALA 2.9 8.7 + - - +
15C ILE* 3.8 3.1 - - - +
16C PRO* 3.3 15.8 - - - +
86D TYR* 4.9 0.2 - - - -
90D CYS* 3.3 48.7 + - - -
93D MET* 3.7 4.2 - - + +
94D ASN* 2.8 20.5 + - - -
104D LYS* 1.3 72.7 - - - +
106D LEU* 1.3 70.0 + - - +
107D LEU* 4.1 3.6 - - + -
266D PHE* 4.0 15.9 - - + -
279D VAL 3.2 5.4 - - - +
280D THR* 2.6 28.6 + - - +
286D MET* 4.1 0.2 - - - -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO* 4.2 6.1 - - + -
19C VAL* 3.3 33.7 - - + -
86D TYR* 3.9 5.8 - - - +
105D THR* 1.3 75.3 - - - +
107D LEU* 1.3 71.2 + - - +
108D VAL* 4.0 10.5 - - + -
117D ASN* 3.8 37.9 - - + +
121D ILE* 4.5 4.3 - - + -
278D GLY* 3.1 3.1 - - - -
279D VAL* 2.7 40.4 + - + +
286D MET* 3.6 16.0 - - + +
294D LEU* 4.1 20.9 - - + -
295D GLY* 5.1 7.2 - - - +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TYR* 3.3 66.9 + - + +
89D LEU* 3.6 31.0 - - + -
90D CYS* 3.8 12.1 - - - +
93D MET* 5.5 0.2 - - + -
105D THR* 4.1 6.7 - - + -
106D LEU* 1.3 77.9 - - - +
108D VAL* 1.3 62.7 + - - +
266D PHE* 3.8 25.6 - - + -
276D LEU* 4.7 3.8 - - + -
277D ALA 3.6 7.9 - - - +
299D ALA* 3.3 17.2 - - - +
300D GLY* 3.8 9.6 - - - -
305D CYS* 4.0 8.7 - - - -
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.0 16.8 - - + -
107D LEU* 1.3 78.1 - - - +
109D THR* 1.3 66.5 + - - +
110D THR 3.8 1.3 - - - +
113D GLU* 3.5 12.3 - - + +
114D ALA* 3.6 29.2 - - - +
117D ASN* 3.5 27.6 - - + +
276D LEU* 3.8 4.3 - - - +
277D ALA* 2.9 38.6 + - + +
278D GLY* 3.8 3.6 - - - +
279D VAL* 5.3 0.7 - - + -
295D GLY 4.8 10.5 - - - +
299D ALA* 4.0 6.5 - - - -
300D GLY 3.2 17.5 + - - -
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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