Contacts of the helix formed by residues 92 - 104 (chain D) in PDB entry 3ESF
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 SER 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D PRO* 1.3 75.3 - - - +
93D GLY* 1.3 70.9 + - - +
94D LYS 3.5 1.6 + - - -
95D LEU 3.9 2.6 + - - -
96D ALA* 3.6 13.7 + - - -
192D GLU* 3.3 22.8 + - - +
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER* 1.3 77.4 + - - +
94D LYS* 1.3 64.1 + - - -
96D ALA* 3.3 3.1 + - - +
97D GLU* 3.2 29.8 + - - +
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Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER 3.5 1.4 + - - -
93D GLY* 1.3 71.9 - - - -
95D LEU* 1.3 57.3 + - - +
97D GLU* 3.5 8.2 + - - +
98D ALA* 3.1 27.5 + - - +
192D GLU* 5.9 0.4 - - - +
195D PHE* 3.8 17.8 - - + -
196D THR* 4.1 22.9 - - + +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PRO* 4.5 2.5 - - + -
92D SER 3.9 1.4 + - - +
93D GLY 3.4 0.4 - - - -
94D LYS* 1.3 78.2 - - - +
96D ALA* 1.3 58.7 + - - +
98D ALA* 4.2 0.4 - - - -
99D ILE* 2.8 39.0 + - + +
128D LEU* 4.7 1.6 - - + -
137D LEU* 3.9 24.0 - - + -
157D ILE* 4.4 7.4 - - + -
188D TRP* 4.1 16.4 - - + -
191D ALA* 3.6 42.0 - - + +
192D GLU* 3.7 23.8 - - + +
195D PHE* 3.8 32.2 - - + -
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLU* 6.1 0.4 - - - +
91D PRO* 3.4 38.0 - - + +
92D SER* 3.6 18.3 + - - -
93D GLY 3.3 3.4 + - - +
95D LEU* 1.3 76.7 - - - +
97D GLU* 1.3 62.6 + - - +
99D ILE* 3.5 4.9 + - - +
100D ARG* 3.2 47.3 + - - +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY* 3.2 17.2 + - - +
94D LYS* 3.8 9.0 - - - +
96D ALA* 1.3 76.7 - - - +
98D ALA* 1.3 57.3 + - - +
100D ARG* 2.8 36.2 + - - +
101D ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LYS 3.1 12.6 + - - +
95D LEU* 3.3 4.2 + - - +
97D GLU* 1.3 72.9 - - - +
99D ILE* 1.3 60.8 + - - +
101D ALA* 3.3 7.1 + - - +
102D SER* 3.0 34.2 + - - +
135D LYS 5.9 1.1 - - - +
137D LEU* 3.6 13.4 - - + +
195D PHE* 3.4 34.5 - - + -
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PRO* 3.9 23.6 - - + -
95D LEU* 2.8 29.9 + - + +
96D ALA* 3.7 7.2 - - - +
98D ALA* 1.3 75.7 - - - +
100D ARG* 1.3 54.5 + - - +
102D SER 3.2 0.7 + - - -
103D PHE* 2.7 39.9 + - + +
105D SER 3.9 8.7 - - - +
106D PHE* 4.0 14.8 - - + +
109D PHE* 3.8 42.0 - - + -
128D LEU* 4.4 8.3 - - + -
137D LEU* 3.8 17.7 - - + -
188D TRP* 4.2 12.1 - - + -
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLU* 5.0 9.1 + - - -
96D ALA* 3.2 37.2 + - - +
97D GLU* 2.8 45.6 + - - +
99D ILE* 1.3 76.0 - - + +
101D ALA* 1.3 58.8 + - - +
104D GLY* 2.8 33.2 + - - +
105D SER* 4.0 24.5 - - - +
106D PHE* 4.5 9.4 - - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU 2.9 17.2 + - - +
98D ALA* 3.3 8.9 + - - +
99D ILE 3.3 0.2 - - - -
100D ARG* 1.3 75.0 - - - +
102D SER* 1.3 59.1 + - - +
136D LYS* 5.5 3.5 - - - +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 3.0 17.2 + - - +
99D ILE 3.9 1.6 - - - -
101D ALA* 1.3 80.0 - - - +
103D PHE* 1.3 66.7 + - - +
135D LYS 4.8 0.5 + - - -
136D LYS* 3.6 28.2 + - - +
137D LEU* 2.8 48.7 + - - +
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ILE* 2.7 31.8 + - + +
102D SER* 1.3 77.0 - - - +
104D GLY* 1.3 57.1 + - - +
105D SER 3.2 17.6 + - - +
108D LYS* 3.4 22.1 - - + +
109D PHE* 3.6 42.8 - + + +
112D GLU* 3.6 26.5 - - - -
128D LEU* 3.9 8.5 - - + -
137D LEU* 3.7 40.8 - - + -
138D LYS* 3.9 11.9 - - - -
139D VAL* 3.9 17.9 - - + -
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 2.8 28.0 + - - +
101D ALA 4.9 0.2 - - - -
102D SER 3.8 0.8 - - - -
103D PHE* 1.3 75.4 - - - +
105D SER* 1.3 63.0 + - - +
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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