Contacts of the helix formed by residues 99 - 104 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94N ILE* 3.5 17.1 + - - +
95N ASN* 3.1 32.1 + - - +
98N ALA* 1.3 78.0 - - + +
100N THR* 1.3 63.2 + - - +
101N TYR 3.5 0.8 + - - -
102N TYR* 3.5 5.7 + - - +
103N MET* 3.0 41.1 + - + +
139N CYS* 6.3 0.2 - - - -
140N PRO 5.1 4.0 - - - +
126P ALA* 3.1 29.3 + - + +
127P GLN* 4.5 0.8 - - + +
130P GLN* 2.9 34.7 + - - +
266P TRP* 3.8 26.3 - - - -
301P PRO* 3.6 26.7 - - + -
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Residues in contact with THR 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M TYR* 3.6 20.6 + - + +
71N MET* 4.6 6.0 - - + +
96N SER* 2.6 28.1 + - - -
97N ALA 3.5 1.0 + - - -
98N ALA 3.2 3.8 + - - -
99N LYS* 1.3 74.3 - - - +
101N TYR* 1.3 72.4 + - - +
103N MET* 3.1 12.6 + - - +
104N SER* 3.1 18.9 + - - -
108N GLN* 3.3 39.9 - - + +
110N VAL* 3.9 12.6 - - + -
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Residues in contact with TYR 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338M HIS* 3.3 26.2 - - + -
339M ILE 3.5 8.5 - - - +
340M TYR* 3.3 32.1 - - - -
341M SER* 3.6 24.8 + - - -
342M SER 4.7 0.5 + - - -
361M SER* 3.2 25.2 + - - -
97N ALA 4.7 2.0 + - - +
98N ALA 4.3 4.4 + - - +
99N LYS 3.5 0.6 - - - -
100N THR* 1.3 78.1 - - - +
102N TYR* 1.3 62.4 + - - +
104N SER* 2.9 19.8 + - - -
106N GLY* 3.1 42.8 + - - -
107N LEU 4.5 0.2 - - - -
108N GLN 3.2 23.9 + - - +
109N PRO* 3.6 18.8 - - + -
110N VAL* 4.8 2.1 - - + +
165N ASN* 5.2 2.7 - - - +
166N PRO* 6.5 0.7 - - + -
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Residues in contact with TYR 102 (chain N).
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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120M LYS* 3.4 39.3 + - + +
335M LEU* 2.9 26.7 + - - +
337M TYR 3.4 22.9 - - - -
338M HIS* 3.1 19.1 + - - +
339M ILE* 4.0 20.5 + - + +
98N ALA 5.1 1.3 + - - +
99N LYS 3.5 4.2 + - - +
100N THR 3.2 0.2 - - - -
101N TYR* 1.3 79.1 - - - +
103N MET* 1.3 69.5 + - + +
105N GLY* 3.1 13.3 + - - -
141N GLY* 6.6 0.2 - - - -
300P VAL* 4.2 10.0 - - + +
301P PRO* 3.0 54.0 + - + -
302P MET 4.2 1.8 - - - -
303P PRO* 3.4 24.3 - - + +
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Residues in contact with MET 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ALA* 3.6 15.5 - - - +
120M LYS* 4.5 10.3 - - - +
121M GLY* 3.8 11.8 + - - -
125M HIS* 3.6 46.5 - - + +
127M TYR* 3.7 21.8 - - + +
95N ASN 4.4 0.2 - - - +
99N LYS* 3.0 28.1 + - + +
100N THR* 3.1 15.0 + - - +
102N TYR* 1.3 81.3 - - + +
104N SER* 1.3 57.7 + - - +
105N GLY 3.2 1.3 - - - -
126P ALA* 3.7 29.4 - - + +
127P GLN* 3.7 23.8 - - - +
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Residues in contact with SER 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M CYS 4.2 0.2 - - - +
117M ALA* 3.8 14.9 - - - +
127M TYR* 3.5 32.1 - - - +
100N THR 3.1 9.5 + - - -
101N TYR 2.9 13.8 + - - -
103N MET* 1.3 78.2 - - - +
105N GLY* 1.3 61.3 + - - +
107N LEU* 2.9 24.3 + - - +
108N GLN* 2.7 33.5 + - - -
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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