Contacts of the helix formed by residues 114 - 122 (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 ALA 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LYS* 2.8 15.2 + - + +
113A ALA* 1.3 71.8 - - - +
115A SER* 1.4 59.5 + - - +
116A GLY 3.1 8.2 + - - -
117A GLU* 4.3 6.6 + - - +
138A PRO* 5.8 0.5 - - - +
197A PRO* 5.5 0.2 - - - +
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Residues in contact with SER 115 (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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113A ALA 3.5 1.2 - - - -
114A ALA* 1.4 75.8 - - - +
116A GLY* 1.3 63.8 + - - +
117A GLU 2.9 4.8 + - - +
118A ALA* 2.9 14.8 + - - +
138A PRO* 3.4 25.9 + - - +
141A ALA* 3.5 17.0 - - - +
142A LYS* 2.9 47.6 + - - +
197A PRO* 5.4 2.0 - - - +
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Residues in contact with GLY 116 (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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113A ALA 4.4 0.2 + - - -
114A ALA 3.1 7.5 + - - -
115A SER* 1.3 76.4 - - - +
117A GLU* 1.3 56.7 + - - +
118A ALA 2.7 6.4 + - - -
119A LYS 3.2 0.2 + - - -
142A LYS* 3.8 2.8 - - - +
188A SER* 2.6 27.2 + - - -
189A PRO* 2.7 26.3 - - - +
195A VAL* 4.0 22.9 - - - +
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Residues in contact with GLU 117 (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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114A ALA 4.3 5.5 + - - +
115A SER* 2.9 1.6 - - - +
116A GLY* 1.3 76.1 - - - +
118A ALA* 1.3 56.6 + - - +
119A LYS 3.3 0.2 - - - -
120A PRO* 2.8 36.1 - - - +
134A ALA* 5.5 5.2 - - + -
135A GLY* 3.8 17.9 - - - -
138A PRO* 3.8 22.7 - - + -
187A LYS* 5.6 0.7 - - - +
188A SER* 3.5 10.7 + - - -
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Residues in contact with ALA 118 (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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115A SER 2.9 15.4 + - - +
116A GLY 2.7 2.8 + - - -
117A GLU* 1.3 78.1 - - - +
119A LYS* 1.3 64.5 + - + +
120A PRO 3.1 1.6 - - - -
121A LYS* 3.1 21.8 + - - +
131A LYS* 4.2 1.9 + - - -
135A GLY 3.7 11.7 - - - -
138A PRO* 4.2 2.2 - - - +
139A LYS* 3.8 31.2 - - + +
142A LYS* 4.6 8.5 - - + -
189A PRO* 5.8 0.7 - - + -
200A ALA* 5.2 5.4 - - + -
203A LYS* 5.1 6.0 + - - +
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Residues in contact with LYS 119 (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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116A GLY 3.2 5.1 + - - -
118A ALA* 1.3 74.0 - - + +
120A PRO* 1.3 62.5 - - - +
121A LYS 2.9 6.3 - - - -
122A ALA* 2.8 18.8 + - - +
123A LYS 3.6 0.5 + - - -
169A VAL* 2.9 43.7 - - + +
172A SER* 4.0 2.6 + - - +
175A LYS* 5.2 1.4 - - - +
177A LYS* 3.5 17.2 - - - +
178A ALA* 2.9 36.6 - - + +
187A LYS 3.2 1.3 - - - -
189A PRO* 3.0 23.1 - - + +
194A ALA* 3.7 15.0 - - - +
199A ALA* 5.1 4.4 + - - +
200A ALA* 5.1 8.2 - - + +
203A LYS* 3.3 40.0 - - - +
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Residues in contact with PRO 120 (chain A).
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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117A GLU* 2.8 37.7 - - - +
118A ALA 3.1 0.6 - - - -
119A LYS* 1.3 82.9 - - - +
121A LYS* 1.3 49.6 + - - +
122A ALA 3.2 0.2 - - - -
123A LYS* 3.2 1.3 - - - +
130A ALA* 3.5 24.2 - - + +
131A LYS* 3.3 12.4 - - + +
135A GLY* 5.7 0.9 - - - -
186A THR 3.6 5.2 - - - +
187A LYS* 2.9 37.0 - - + +
188A SER* 3.3 8.5 - - - +
216A LYS* 2.7 40.4 + - - -
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Residues in contact with LYS 121 (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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118A ALA 3.3 9.9 - - - +
120A PRO* 1.3 77.3 - - - +
122A ALA* 1.3 70.4 + - - +
123A LYS 3.1 1.2 + - - -
131A LYS* 2.9 35.8 - - - +
139A LYS* 3.9 27.4 - - + +
181A LYS* 5.1 3.8 - - - -
203A LYS* 3.7 32.9 - - - +
204A ALA* 4.4 8.5 + - - +
207A PRO* 4.5 12.9 - - - +
214A ALA 4.1 5.2 - - - +
215A ALA* 2.9 42.2 - - + +
216A LYS* 2.9 25.4 + - - +
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Residues in contact with ALA 122 (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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76A GLU* 5.2 0.2 - - - +
119A LYS* 2.8 19.2 + - + +
121A LYS* 1.3 79.1 - - - +
123A LYS* 1.3 65.7 + - - +
169A VAL* 3.2 18.8 - - + -
178A ALA* 4.6 2.2 - - + +
181A LYS* 2.9 48.8 - - + +
182A PRO* 4.6 4.0 - - + +
185A ALA* 4.3 3.7 - - - +
203A LYS* 4.3 13.5 - - - -
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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