Contacts of the helix formed by residues 99 - 104 (chain X) in PDB entry 3EXG
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 99 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84V ASN* 4.8 0.8 + - - -
126V ALA* 2.9 41.8 + - + +
127V GLN* 4.1 2.8 - - + +
130V GLN* 2.7 34.2 + - - +
266V TRP* 4.1 15.7 - - + -
301V PRO* 3.8 25.6 - - + -
94X ILE* 3.4 22.6 + - - +
95X ASN* 3.0 27.5 + - - +
96X SER 4.8 0.6 - - - -
97X ALA 3.4 1.2 - - - +
98X ALA* 1.3 77.5 - - + +
100X THR* 1.3 58.8 + - - +
101X TYR 3.7 0.9 - - - -
102X TYR* 3.7 4.9 + - - +
103X MET* 2.9 37.1 + - + +
140X PRO 4.9 3.6 - - - +
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Residues in contact with THR 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127W TYR* 3.9 16.5 + - + +
71X MET* 4.6 6.2 - - + +
96X SER* 2.7 30.9 + - - -
97X ALA 3.5 1.6 + - - -
98X ALA 3.4 4.0 - - - -
99X LYS* 1.3 75.3 - - - +
101X TYR* 1.3 66.8 + - - +
103X MET* 3.8 16.2 - - - +
104X SER* 2.9 25.5 + - - -
108X GLN* 3.4 35.9 - - + +
110X VAL* 4.0 11.2 - - + -
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Residues in contact with TYR 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338W HIS* 3.5 19.1 - - - -
339W ILE 4.1 9.0 - - - +
340W TYR* 3.2 24.9 - - - -
341W SER* 3.4 30.0 + - - +
342W SER 4.5 0.5 + - - -
361W SER* 2.8 33.3 + - - -
97X ALA 5.0 1.4 + - - -
98X ALA 4.9 2.1 + - - +
99X LYS 3.7 0.2 - - - -
100X THR* 1.3 75.9 - - - +
102X TYR* 1.3 64.4 + - - +
104X SER* 3.0 6.8 + - - -
106X GLY* 2.9 58.3 + - - -
108X GLN 3.6 8.3 + - - +
109X PRO* 3.6 32.8 - - + -
110X VAL* 5.3 1.9 - - - +
165X ASN* 5.5 1.6 - - - +
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Residues in contact with TYR 102 (chain X).
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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300V VAL* 3.9 15.1 - - + +
301V PRO* 3.2 50.0 + - + -
302V MET 4.6 0.9 - - - -
303V PRO* 3.5 27.1 - - + +
120W LYS* 3.5 37.9 + - + +
335W LEU* 3.0 29.1 + - - +
336W GLY 4.5 0.2 - - - -
337W TYR 3.8 12.1 - - - -
338W HIS* 3.1 22.4 + - - +
339W ILE* 3.8 22.3 + - + +
98X ALA 5.4 1.5 + - - +
99X LYS* 3.7 4.6 + - - +
100X THR 3.2 0.2 - - - -
101X TYR* 1.3 80.8 - - - +
103X MET* 1.3 68.7 + - + +
104X SER 3.1 0.9 + - - -
105X GLY* 3.3 8.5 + - - -
141X GLY* 6.4 0.7 - - - -
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Residues in contact with MET 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126V ALA* 4.0 23.8 - - + +
127V GLN* 3.8 28.9 - - - +
302V MET 5.7 0.4 - - - +
117W ALA* 3.9 4.0 - - - +
120W LYS* 4.6 3.3 - - - +
121W GLY* 3.6 30.2 + - - +
125W HIS* 3.4 47.2 - - + +
127W TYR* 3.8 15.7 - - - +
95X ASN 4.3 2.7 - - - +
99X LYS* 2.9 29.4 + - + +
100X THR* 3.4 20.6 + - - +
102X TYR* 1.3 77.9 - - + +
104X SER* 1.3 58.4 + - - +
105X GLY 3.2 1.5 + - - -
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Residues in contact with SER 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116W CYS 4.9 0.2 - - - +
117W ALA* 4.0 11.0 - - - +
127W TYR* 3.5 35.7 - - - +
100X THR 2.9 18.1 + - - -
101X TYR* 3.0 6.6 + - - -
103X MET* 1.3 76.9 - - - +
105X GLY* 1.3 61.8 + - - +
107X LEU* 3.1 34.6 + - - +
108X GLN* 3.2 15.6 + - - -
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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