Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 1EFU
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 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PRO 4.9 0.2 - - - +
112A MET* 1.3 87.4 - - + +
114A GLN* 1.3 65.0 + - - +
115A THR 3.3 0.3 + - - -
116A ARG* 3.2 32.7 - - - +
117A GLU* 3.2 2.3 - - - +
16B GLY* 4.9 7.6 - - - +
85B ASP* 3.2 23.6 - - - +
124B LYS* 3.1 51.8 - - + +
125B ILE* 4.2 5.6 - - + -
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 2.9 24.2 + - + -
112A MET* 3.4 9.1 - - + +
113A PRO* 1.3 90.3 - - - +
115A THR* 1.3 60.5 + - - +
116A ARG 3.1 3.1 - - - -
117A GLU* 2.9 29.6 + - - +
118A HIS* 3.0 33.0 + - + +
81B PHE* 4.2 12.8 - - + +
82B VAL* 3.5 34.1 - - + +
85B ASP* 3.7 2.6 + - - +
125B ILE* 2.8 31.5 + - - +
127B GLU* 4.0 2.9 + - - +
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 6.0 0.2 - - - +
103A LEU* 4.1 22.2 - - + -
105A VAL* 4.7 8.9 - - + +
111A PRO* 3.7 11.5 - - + +
112A MET* 2.8 41.3 + - - +
114A GLN* 1.3 79.3 - - - +
116A ARG* 1.3 56.5 + - - +
118A HIS* 3.2 14.5 + - - +
119A ILE* 3.0 36.3 + - + +
153A VAL* 6.1 0.9 - - + -
156A LEU* 3.9 18.8 - - + -
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Residues in contact with ARG 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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112A MET 4.3 0.2 + - - -
113A PRO* 3.2 20.6 + - - +
115A THR* 1.3 78.1 - - - +
117A GLU* 1.3 74.0 + - - +
119A ILE* 3.9 5.6 - - - +
120A LEU* 2.9 33.4 + - - +
156A LEU* 3.8 22.1 - - + +
159A GLN* 2.6 31.3 + - - +
160A TYR* 3.0 36.4 + - + +
85B ASP* 5.1 2.2 - - - -
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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
----------------------------------------------------------
84A HIS* 4.5 3.3 - - + -
113A PRO 3.2 14.0 - - - +
114A GLN* 2.9 12.5 + - - +
116A ARG* 1.3 87.9 - - - +
118A HIS* 1.3 61.1 + - - +
120A LEU* 3.8 19.8 - - + +
121A LEU* 3.3 15.8 + - - +
160A TYR* 5.5 0.2 + - - -
81B PHE* 3.0 47.9 - - + +
84B LYS* 3.9 22.7 - - + +
85B ASP* 2.8 33.4 - - - +
86B ALA 5.0 1.2 + - - -
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.4 36.0 - - + +
18A GLY* 3.4 37.7 + - - -
19A HIS* 3.5 7.2 - - + -
103A LEU* 4.1 12.8 - - + +
114A GLN* 3.0 31.4 + - + +
115A THR* 3.4 18.3 + - - +
116A ARG 3.2 0.4 - - - -
117A GLU* 1.3 75.1 - - - +
119A ILE* 1.3 65.1 + - - +
121A LEU* 3.2 2.9 + - - +
122A GLY* 3.2 15.9 + - - -
130A ILE* 5.7 0.2 - - - +
79B THR* 5.6 0.6 + - - -
81B PHE* 3.4 43.2 - + - +
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Residues in contact with ILE 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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103A LEU* 4.2 19.3 - - + -
115A THR* 3.0 25.5 + - + +
116A ARG* 4.0 5.4 - - - +
118A HIS* 1.3 74.6 - - - +
120A LEU* 1.3 51.2 + - - +
122A GLY* 2.9 4.7 + - - -
123A ARG* 2.8 30.8 + - - +
130A ILE* 4.8 8.5 - - + -
153A VAL* 5.0 0.9 - - + +
156A LEU* 3.6 34.1 - - + +
157A LEU* 4.0 21.5 - - + +
160A TYR* 3.6 22.4 - - + -
162A PHE* 3.6 28.8 - - + -
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Residues in contact with LEU 120 (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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84A HIS* 5.8 3.4 - - + +
116A ARG 2.9 20.3 + - - +
117A GLU* 3.8 22.9 - - + +
118A HIS 3.3 0.2 - - - -
119A ILE* 1.3 73.0 - - - +
121A LEU* 1.3 61.3 + - - +
123A ARG* 3.6 10.7 - - + +
124A GLN* 2.8 33.1 + - + +
160A TYR* 3.8 31.6 - - + +
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Residues in contact with LEU 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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17A ILE* 3.9 10.3 - - + -
81A CYS* 4.9 3.1 - - + -
84A HIS* 3.5 39.7 - - + +
87A TYR* 4.1 21.8 - - + -
88A VAL* 3.8 14.8 - - + -
98A MET* 6.1 2.5 - - + -
117A GLU 3.3 6.2 + - - +
118A HIS 3.2 7.9 + - - +
119A ILE 3.2 0.6 - - - -
120A LEU* 1.3 75.7 - - - +
122A GLY* 1.3 70.6 + - - +
124A GLN* 3.1 5.1 + - + -
125A VAL* 2.9 46.3 + - + +
81B PHE* 3.5 28.3 - - + -
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Residues in contact with GLY 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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17A ILE* 5.2 2.2 - - - +
98A MET* 5.7 1.1 - - - -
118A HIS 3.2 6.8 + - - -
119A ILE 2.9 8.1 + - - -
121A LEU* 1.3 83.0 - - - +
123A ARG* 1.3 58.6 + - - +
125A VAL* 4.5 0.4 - - - -
126A GLY 3.4 1.2 + - - -
127A VAL* 3.0 47.8 + - - +
130A ILE* 4.6 7.4 - - - -
162A PHE* 3.7 10.7 - - - -
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Residues in contact with ARG 123 (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 ILE 2.8 11.2 + - - +
120A LEU* 3.6 16.2 - - + +
121A LEU 3.1 0.2 - - - -
122A GLY* 1.3 75.6 - - - +
124A GLN* 1.3 59.3 + - - +
126A GLY* 2.9 29.9 + - - -
127A VAL 3.9 9.3 + - - -
128A PRO* 5.7 1.2 + - - +
160A TYR* 3.0 34.3 + - + +
161A ASP* 3.3 33.3 + - - +
162A PHE* 3.6 40.3 - - + -
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A HIS* 3.0 37.7 + - - -
88A VAL* 4.2 12.0 - - - +
91A MET* 5.5 0.2 - - - +
120A LEU* 2.8 25.1 + - + +
121A LEU* 3.1 6.0 + - - +
123A ARG* 1.3 74.8 - - - +
125A VAL* 1.3 60.3 + - + +
126A GLY 3.6 1.6 + - - -
307A GLU* 3.6 33.1 + - - +
357A LYS* 3.7 23.8 + - - +
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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