Contacts of the helix formed by residues 99 - 104 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F ILE* 3.2 24.3 + - - +
95F ASN* 3.3 35.6 + - - +
97F ALA 3.2 1.2 + - - -
98F ALA* 1.3 75.1 - - + +
100F THR* 1.3 64.0 + - - +
101F TYR 3.6 0.9 - - - -
102F TYR* 3.6 6.2 + - - +
103F MET* 3.1 34.3 + - + +
139F CYS* 6.1 0.2 - - - -
140F PRO 5.2 4.9 - - - +
84H ASN* 5.0 0.4 + - - -
87H MET* 4.9 0.4 - - - +
126H ALA* 3.2 28.8 + - + +
127H GLN* 4.5 2.4 - - + +
130H GLN* 3.1 37.4 + - - +
266H TRP* 3.9 18.2 - - - -
301H PRO* 3.8 25.1 - - + -
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Residues in contact with THR 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E TYR* 4.0 17.9 + - + +
71F MET* 4.3 7.5 - - + +
95F ASN 4.0 0.5 + - - -
96F SER* 2.6 30.6 + - - -
97F ALA 3.1 9.4 + - - -
98F ALA 3.3 0.6 - - - -
99F LYS* 1.3 75.0 - - - +
101F TYR* 1.3 70.0 + - - +
102F TYR 3.2 0.3 + - - -
103F MET* 3.3 17.5 + - - +
104F SER* 3.2 17.8 + - - -
108F GLN* 3.4 35.4 - - + +
110F VAL* 4.1 6.1 - - + -
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Residues in contact with TYR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E HIS* 3.6 15.0 - - - -
339E ILE 3.6 22.9 - - - +
340E TYR 3.3 25.1 - - - -
341E SER* 3.4 23.4 + - - -
342E SER 4.7 0.7 + - - -
361E SER 2.6 23.6 + - - -
97F ALA 4.5 2.7 + - - +
98F ALA 4.8 2.4 + - - +
100F THR* 1.3 80.8 - - - +
102F TYR* 1.3 60.7 + - - +
104F SER* 3.1 5.1 + - - -
106F GLY* 3.1 55.2 + - - -
108F GLN 3.3 24.0 + - - +
109F PRO* 3.5 21.1 - - + -
110F VAL* 4.8 2.9 - - + +
165F ASN* 4.7 4.0 - - - +
166F PRO* 6.5 0.9 - - + -
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Residues in contact with TYR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LYS* 3.5 37.7 + - + +
335E LEU* 2.7 27.9 + - - -
336E GLY* 4.5 3.4 - - - -
337E TYR 3.2 20.4 - - - -
338E HIS* 3.0 30.3 + - - +
339E ILE* 4.2 8.8 + - + +
98F ALA 5.4 0.4 + - - -
99F LYS 3.6 3.9 + - - +
100F THR 3.2 0.4 - - - -
101F TYR* 1.3 75.1 - - - +
103F MET* 1.3 69.7 - - + +
104F SER 2.9 3.2 + - - -
105F GLY* 3.1 13.2 + - - -
300H VAL* 4.3 5.3 - - + +
301H PRO* 3.0 60.8 + - + -
302H MET 4.5 1.6 - - - -
303H PRO* 3.9 20.9 - - + +
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Residues in contact with MET 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ALA* 3.7 2.6 - - - +
120E LYS* 4.8 8.5 - - - +
121E GLY* 3.4 27.1 + - - -
125E HIS* 3.6 33.9 - - + +
127E TYR* 3.8 17.0 - - + +
99F LYS* 3.1 26.7 + - + +
100F THR* 3.7 19.5 - - - +
102F TYR* 1.3 82.6 - - + +
104F SER* 1.3 58.6 + - - +
105F GLY 3.3 0.9 - - - -
125H ALA* 6.0 0.2 - - + -
126H ALA* 3.7 26.0 - - + +
127H GLN* 3.6 41.7 - - - +
302H MET 5.5 0.4 - - - +
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Residues in contact with SER 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E CYS 4.4 1.0 - - - +
117E ALA* 4.0 17.2 - - - +
127E TYR* 3.3 36.9 - - - +
100F THR 3.2 9.6 + - - -
101F TYR 3.1 8.3 + - - -
102F TYR 2.9 1.6 + - - -
103F MET* 1.3 76.1 - - - +
105F GLY* 1.3 59.9 + - - +
107F LEU* 3.1 22.2 + - - +
108F GLN* 3.0 30.2 + - - +
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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