Contacts of the helix formed by residues 99 - 104 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84N ASN* 5.2 0.6 + - - -
87N MET* 4.9 0.4 - - - +
126N ALA* 3.2 30.2 + - - +
127N GLN* 4.3 2.3 - - + +
130N GLN* 3.0 28.5 + - - +
266N TRP* 3.9 25.1 - - - -
301N PRO* 3.9 22.2 - - + +
94P ILE* 3.3 21.5 + - - +
95P ASN* 2.9 34.6 + - - +
97P ALA 3.2 0.8 - - - -
98P ALA* 1.3 82.1 - - + +
100P THR* 1.3 65.1 + - - +
101P TYR 3.4 1.5 + - - -
102P TYR* 3.4 8.2 + - - +
103P MET* 3.0 33.0 + - + +
139P CYS* 6.4 0.2 - - - -
140P PRO 4.8 3.8 - - - +
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Residues in contact with THR 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O TYR* 3.9 15.6 + - + +
71P MET* 4.3 8.2 - - + +
95P ASN 4.4 0.2 + - - -
96P SER* 2.7 29.7 + - - -
97P ALA 3.6 1.8 + - - -
98P ALA 3.6 1.2 - - - -
99P LYS* 1.3 74.2 - - - +
101P TYR* 1.3 70.5 + - - +
103P MET* 3.0 18.5 + - - +
104P SER* 2.8 22.0 + - - -
108P GLN* 3.3 39.3 - - + +
110P VAL* 4.1 9.9 - - + -
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Residues in contact with TYR 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338O HIS* 3.2 25.1 - - + -
339O ILE 4.0 7.6 - - - +
340O TYR 3.2 33.4 - - - -
341O SER* 3.4 24.3 + - - -
342O SER 4.9 0.3 + - - -
361O SER* 2.9 23.4 + - - -
97P ALA 4.7 2.8 + - - -
98P ALA 4.7 2.3 + - - +
99P LYS 3.4 0.8 - - - -
100P THR* 1.3 75.6 - - - +
102P TYR* 1.3 63.2 + - - +
104P SER* 2.9 17.9 + - - -
105P GLY 3.0 6.6 + - - -
106P GLY* 2.9 41.7 + - - -
108P GLN 3.5 30.0 + - - +
109P PRO* 3.7 11.4 - - + -
110P VAL* 5.2 2.6 - - + +
165P ASN* 5.1 3.8 - - - +
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Residues in contact with TYR 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300N VAL* 4.1 14.5 - - + +
301N PRO* 3.1 62.0 + - + -
302N MET 4.3 1.6 - - - -
303N PRO* 3.4 30.8 - - + +
120O LYS* 3.5 30.7 - - + +
335O LEU* 3.0 28.6 + - - +
336O GLY 4.7 0.4 - - - -
337O TYR 3.7 19.7 - - - -
338O HIS* 3.2 16.5 + - - +
339O ILE* 3.9 18.7 + - + +
98P ALA 5.4 1.5 + - - +
99P LYS 3.4 3.7 + - - +
100P THR 3.2 0.4 - - - -
101P TYR* 1.3 79.4 - - - +
103P MET* 1.3 65.8 + - + +
105P GLY* 3.2 12.3 + - - -
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Residues in contact with MET 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N ALA* 3.9 25.4 - - + +
127N GLN* 3.6 31.2 - - - +
117O ALA* 3.7 15.6 - - - +
120O LYS* 5.0 2.7 - - - +
121O GLY* 3.7 18.1 + - - -
125O HIS* 3.6 42.4 - - + +
127O TYR* 3.6 23.1 - - - +
95P ASN 4.0 3.4 - - - +
99P LYS* 3.0 14.6 + - - +
100P THR* 3.0 28.0 + - - +
102P TYR* 1.3 75.8 - - + +
104P SER* 1.3 58.3 - - - +
105P GLY 3.0 8.2 + - - -
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Residues in contact with SER 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O CYS 4.6 0.7 - - - +
117O ALA* 4.3 9.6 - - - +
127O TYR* 3.6 32.1 - - - +
100P THR 2.8 11.7 + - - -
101P TYR 2.9 14.6 + - - -
103P MET* 1.3 75.9 - - - +
105P GLY* 1.3 61.7 + - - +
106P GLY 3.3 0.2 + - - -
107P LEU* 3.3 21.9 + - - +
108P GLN* 3.2 36.4 + - - +
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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