Contacts of the helix formed by residues 100 - 107 (chain A) in PDB entry 2FE2
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 GLY 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.0 13.2 + - - +
98A THR* 3.2 7.9 + - - -
99A LYS* 1.4 80.3 - - - +
101A THR* 1.3 59.6 + - - +
102A GLY 3.3 2.7 - - - -
103A ALA* 3.2 13.5 + - - +
104A SER* 2.9 31.1 + - - -
149A LYS* 4.8 2.8 + - - -
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 3.3 39.3 + - - +
95A LEU* 3.5 4.1 + - - +
96A VAL* 3.3 24.3 + - - +
99A LYS* 3.5 5.2 - - - +
100A GLY* 1.3 78.3 - - - +
102A GLY* 1.3 64.3 + - - +
104A SER 3.2 0.7 + - - -
105A GLY* 3.0 20.8 + - - -
156A LYS* 3.6 21.0 - - - +
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 4.9 12.1 - - - +
100A GLY* 3.3 0.6 - - - -
101A THR* 1.3 80.1 - - - +
103A ALA* 1.3 62.2 + - - +
105A GLY* 3.4 1.7 + - - -
106A SER* 3.0 24.8 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 5.7 1.4 - - - +
100A GLY* 3.2 16.4 + - - +
101A THR 3.2 0.4 - - - -
102A GLY* 1.3 76.4 - - - +
104A SER* 1.3 62.6 + - - +
106A SER* 2.6 24.9 + - - -
107A PHE* 3.5 4.0 + - - +
149A LYS* 4.9 8.5 - - - +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.5 4.5 - - - -
100A GLY 2.9 14.7 + - - -
101A THR 3.2 0.2 + - - -
103A ALA* 1.3 77.1 - - - +
105A GLY* 1.3 62.2 + - - +
107A PHE* 3.0 23.3 + - - +
149A LYS* 4.1 26.6 + - - +
152A LYS* 4.4 3.5 - - - +
153A LYS* 3.3 19.2 + - - +
156A LYS* 3.0 37.4 + - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR 3.0 14.3 + - - -
102A GLY* 3.9 1.8 - - - -
104A SER* 1.3 76.8 - - - +
106A SER* 1.3 61.5 + - - +
107A PHE 3.1 8.3 + - - +
153A LYS* 4.4 11.8 - - - -
156A LYS* 3.5 13.4 - - - +
157A LYS* 6.5 0.4 - - - -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 3.0 13.8 + - - -
103A ALA* 2.6 23.3 + - - -
105A GLY* 1.3 73.9 - - - +
107A PHE* 1.3 65.6 + - - +
108A LYS* 3.2 4.9 + - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 3.5 2.6 + - - +
104A SER* 3.0 20.3 + - - +
105A GLY 3.4 8.5 - - - +
106A SER* 1.3 81.6 + - - +
108A LYS* 1.3 99.4 + - + +
109A LEU* 3.5 1.9 + - - +
147A ALA* 4.2 19.5 - - + -
149A LYS* 4.0 21.1 - - + -
150A ALA* 3.2 42.8 - - + -
153A LYS* 4.2 13.6 - - + -
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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