Contacts of the helix formed by residues 154 - 161 (chain A) in PDB entry 1EF1
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 PRO 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.4 34.3 - - + +
111A LEU* 3.5 18.4 - - + +
113A ASP* 4.4 7.6 - - + +
117A CYS* 5.3 0.7 - - + +
122A ALA* 4.0 20.4 - - + -
153A LEU* 1.3 88.9 - - + +
155A GLN* 1.3 64.9 + - - +
156A ARG* 4.1 28.9 - - - +
157A VAL* 3.1 19.4 + - + +
158A LEU* 3.4 9.7 + - - +
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Residues in contact with GLN 155 (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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111A LEU 4.4 1.4 + - - -
113A ASP* 5.6 0.6 + - - +
151A LYS* 4.3 11.8 + - - +
153A LEU 3.5 2.6 + - - -
154A PRO* 1.3 70.5 - - - +
156A ARG* 1.3 57.3 + - - +
158A LEU* 3.1 29.0 + - - +
159A GLU* 2.9 57.7 + - - +
576D SER 6.0 2.2 - - - +
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Residues in contact with ARG 156 (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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110A ILE 5.2 0.2 + - - -
113A ASP* 2.8 48.7 + - - +
115A ILE 4.8 0.8 + - - -
116A TYR* 3.7 17.3 + - - +
117A CYS* 3.0 41.9 + - - +
118A PRO* 4.7 1.6 - - - +
119A PRO* 4.7 1.4 - - - +
154A PRO* 3.2 16.1 - - + +
155A GLN* 1.3 77.6 - - - +
157A VAL* 1.3 75.5 + - - +
159A GLU* 3.4 12.4 + - - +
160A GLN* 2.9 45.3 + - - +
539C THR* 3.9 32.8 - - + -
541C ASN* 5.8 0.2 - - - -
542C ASP* 3.9 11.7 + - - -
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Residues in contact with VAL 157 (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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119A PRO* 4.0 28.0 - - + +
122A ALA* 4.1 6.5 - - + -
123A VAL* 5.1 0.7 - - + -
153A LEU* 4.3 14.8 - - + -
154A PRO* 3.1 28.6 + - + +
156A ARG* 1.3 95.0 - - - +
158A LEU* 1.3 65.0 + - - +
160A GLN* 3.3 9.7 + - - -
161A HIS* 2.9 44.0 + - + +
168A TRP* 4.0 16.7 - - + -
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Residues in contact with LEU 158 (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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151A LYS* 6.0 0.4 - - - +
153A LEU* 3.6 37.9 - - + +
154A PRO 3.6 10.3 - - - +
155A GLN* 3.1 32.5 + - - +
157A VAL* 1.3 76.2 - - - +
159A GLU* 1.3 61.8 + - - +
161A HIS 3.2 18.9 - - - +
163A LEU 4.9 2.4 - - - +
168A TRP* 3.4 33.3 + - + +
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Residues in contact with GLU 159 (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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155A GLN* 2.9 45.4 + - - +
156A ARG* 3.8 12.2 + - - +
157A VAL 3.3 0.4 - - - -
158A LEU* 1.3 76.5 - - - +
160A GLN* 1.3 62.2 + - + +
161A HIS 3.8 1.7 + - - +
534C ASP* 5.1 0.3 - - - +
537C LYS* 4.0 26.2 + - + +
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Residues in contact with GLN 160 (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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119A PRO* 3.9 14.7 - - - +
156A ARG* 2.9 27.7 + - - +
157A VAL* 3.3 3.3 + - - -
158A LEU 3.3 0.6 - - - -
159A GLU* 1.3 79.9 - - + +
161A HIS* 1.3 65.5 + - - +
533C ARG* 2.9 44.3 + - - +
534C ASP* 2.7 30.9 + - - +
537C LYS* 3.5 20.5 + - + +
538C LYS* 4.0 3.2 - - - +
539C THR* 4.0 4.0 - - + +
542C ASP* 2.5 31.6 + - - +
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Residues in contact with HIS 161 (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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119A PRO* 3.7 31.1 - - + +
157A VAL* 2.9 31.7 + - + +
158A LEU 3.2 14.2 - - - +
159A GLU 3.5 1.9 - - - +
160A GLN* 1.3 81.8 - - + +
162A LYS* 1.3 59.8 + - - +
163A LEU* 2.9 15.4 + - + +
168A TRP* 3.7 22.4 + + + -
529C LEU* 3.9 33.4 - - + +
532C ALA* 3.3 13.2 - - + +
533C ARG* 3.8 39.4 + - - +
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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