Contacts of the helix formed by residues 98 - 112 (chain B) in PDB entry 1EFP
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A MET* 4.1 12.3 - - + -
400A AMP 3.8 12.8 - - + +
95B ASP* 5.7 0.2 - - - +
96B ILE 3.8 3.1 - - - +
97B GLU* 1.3 86.2 - - + +
99B LEU* 1.3 56.1 + - - +
101B VAL* 3.9 6.6 - - + +
102B ALA* 2.9 30.0 + - - +
126B ASN* 4.2 5.4 - - - +
128B MET* 3.6 35.4 - - + -
131B THR* 3.2 31.9 + - - +
134B MET* 3.8 19.9 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 4.6 15.5 - - + +
107A ASP* 4.3 7.0 - - - +
108A VAL* 4.0 8.3 - - - +
109A MET* 3.6 33.3 - - + +
97B GLU* 2.8 4.8 + - + +
98B PRO* 1.3 77.6 - - - +
100B ALA* 1.3 65.7 + - - +
102B ALA* 3.5 2.9 + - - +
103B LYS* 3.1 47.6 + - - +
134B MET* 3.8 21.6 - - + -
138B ILE* 5.0 6.1 - - + -
218B ARG* 3.8 44.6 - - + +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 4.7 5.2 - - + -
97B GLU* 2.7 24.6 + - + +
99B LEU* 1.3 71.4 - - - +
101B VAL* 1.3 66.5 + - - +
103B LYS* 3.1 9.1 + - - +
104B ILE* 3.0 28.1 + - - +
213B VAL* 4.1 5.0 - - + +
214B ASP 4.6 4.5 - - - +
215B VAL* 4.2 35.9 - - + +
216B ALA 5.4 3.1 - - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A AMP 3.7 39.5 - - + +
63B ILE* 4.1 10.1 - - + -
96B ILE* 3.5 34.5 - - + +
97B GLU 3.0 12.2 + - - +
98B PRO* 4.0 9.4 - - + +
100B ALA* 1.3 76.8 - - - +
102B ALA* 1.3 57.1 + - - +
104B ILE* 3.1 3.6 + - - +
105B LEU* 2.8 55.7 + - + +
131B THR* 3.8 8.3 - - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO 2.9 20.5 + - - +
99B LEU* 3.7 4.9 - - - +
100B ALA 3.2 0.2 - - - -
101B VAL* 1.3 77.1 - - - +
103B LYS* 1.3 56.3 + - - +
105B LEU* 4.5 5.2 - - - -
106B ALA* 2.9 31.9 + - - +
131B THR* 4.2 4.9 - - - +
134B MET* 3.8 23.6 - - + -
135B LEU* 3.3 20.1 - - - +
138B ILE* 3.8 13.5 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP* 3.0 32.6 + - - -
99B LEU* 3.1 28.8 + - - +
100B ALA* 3.1 9.9 + - - +
102B ALA* 1.3 76.7 - - - +
104B ILE* 1.3 59.5 + - - +
106B ALA* 3.7 5.5 - - - +
107B ALA* 3.4 18.9 + - - +
138B ILE* 3.4 21.3 - - + -
213B VAL* 4.1 25.7 - - + +
218B ARG* 3.9 13.3 - - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.4 42.2 - - + -
86B VAL* 3.9 29.4 - - + -
96B ILE* 4.8 0.7 - - + -
100B ALA 3.0 16.0 + - - +
101B VAL* 3.4 5.8 - - - +
103B LYS* 1.3 74.0 - - - +
105B LEU* 1.3 61.2 + - - +
106B ALA 3.0 1.1 - - - -
107B ALA* 2.9 21.2 + - - +
108B VAL* 2.9 15.4 + - + +
208B ALA* 4.5 6.1 - - + -
211B TYR* 4.1 13.5 - - + -
213B VAL* 3.9 20.9 - - + -
215B VAL* 4.2 21.8 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A AMP 5.2 1.8 - - + -
4B LEU* 4.1 6.2 - - + +
6B PRO* 4.2 31.0 - - + -
61B VAL* 4.5 19.7 - - + -
63B ILE* 3.5 30.1 - - + -
101B VAL* 2.8 36.8 + - + +
102B ALA* 4.5 0.7 - - - -
104B ILE* 1.3 73.8 - - + +
106B ALA* 1.3 52.8 + - - +
108B VAL* 3.7 6.6 - - - +
109B ALA* 2.7 37.1 + - - +
131B THR* 3.9 16.6 - - + -
135B LEU* 3.7 25.1 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA 2.9 17.4 + - - +
103B LYS 3.7 6.7 - - - +
105B LEU* 1.3 78.8 - - - +
107B ALA* 1.3 56.2 + - - +
109B ALA* 3.8 1.3 - - - +
110B ARG* 3.0 40.5 + - - +
135B LEU* 3.5 6.5 - - + +
138B ILE* 3.8 21.8 - - + -
139B LEU* 3.7 25.2 - - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS 3.4 9.2 + - - +
104B ILE 2.9 9.4 + - - +
106B ALA* 1.3 75.7 - - - +
108B VAL* 1.3 61.6 + - - +
110B ARG* 3.4 8.8 + - - +
111B ALA* 2.9 31.8 + - - +
211B TYR* 3.6 37.0 - - + +
213B VAL* 5.4 0.4 - - + -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.2 20.2 - - + -
61B VAL* 4.6 12.8 - - + -
84B ILE* 4.0 25.1 - - + -
86B VAL* 4.6 6.5 - - + -
104B ILE* 2.9 25.0 + - + +
105B LEU* 3.7 9.9 - - - +
107B ALA* 1.3 76.4 - - - +
109B ALA* 1.3 57.0 + - - +
111B ALA* 3.3 2.8 + - - -
112B GLU* 2.8 40.8 + - + +
211B TYR* 3.6 35.4 - - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.9 5.6 - - + -
105B LEU 2.7 22.7 + - - +
106B ALA* 3.8 6.1 - - - +
108B VAL* 1.3 74.6 - - - +
110B ARG* 1.3 61.3 + - - +
113B GLY* 3.2 3.1 + - - -
114B THR* 3.0 46.6 + - - +
117B ILE* 3.6 24.2 - - + -
139B LEU* 4.7 7.0 - - + -
141B TRP* 4.8 6.0 - - + -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA* 3.0 28.8 + - - +
107B ALA* 3.7 7.0 - - - +
109B ALA* 1.3 75.0 - - - +
111B ALA* 1.3 62.8 + - - +
113B GLY* 3.6 9.2 + - - -
138B ILE* 4.1 18.6 + - - +
139B LEU* 3.7 32.4 + - + +
141B TRP* 6.1 2.5 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 2.9 18.7 + - - +
108B VAL* 3.8 5.2 - - - +
110B ARG* 1.3 79.8 - - - +
112B GLU* 1.3 70.1 + - - +
113B GLY 3.2 1.2 + - - -
206B LYS* 6.0 2.0 - - - +
211B TYR* 5.1 9.0 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 3.5 27.7 + - - +
4B LEU* 5.5 0.2 - - + -
59B ILE* 4.8 11.7 - - + -
82B ARG* 2.9 41.3 + - - +
84B ILE* 3.9 21.2 - - + +
108B VAL* 2.8 29.0 + - + +
111B ALA* 1.3 83.1 - - - +
113B GLY* 1.3 63.6 + - - +
114B THR* 3.5 15.2 + - + -
206B LYS* 5.4 4.9 + - - -
211B TYR* 5.2 3.3 + - - -
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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