Contacts of the helix formed by residues 136 - 141 (chain D) in PDB entry 3SDL
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 136 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D HIS* 3.5 48.0 - - + +
41D PHE* 3.8 15.3 - - + -
100D LEU 3.6 13.0 - - - +
101D THR 4.2 9.2 - - - +
102D GLN 3.5 8.3 - - - +
103D THR* 4.2 5.1 - - + -
134D GLN 4.3 1.8 - - - +
135D LEU* 1.3 96.8 - - + +
137D LEU* 1.3 61.5 + - - +
139D GLU* 3.0 33.3 - - + +
140D TYR* 3.8 5.4 - - - -
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Residues in contact with LEU 137 (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 VAL* 3.7 33.9 - - + -
99D ARG 3.5 18.8 - - - +
100D LEU* 3.2 13.2 + - + +
102D GLN* 2.9 26.7 + - + +
103D THR 3.8 1.8 - - - +
104D VAL* 3.8 36.3 - - + -
107D LEU* 3.9 24.9 - - + -
131D LEU* 5.3 1.1 - - + -
136D PRO* 1.3 67.0 - - - +
138D GLY* 1.3 61.9 + - - +
139D GLU 3.0 7.1 + - - -
140D TYR* 3.1 20.4 + - + +
141D GLY 4.0 1.2 + - - -
142D LEU* 4.0 25.0 - - + +
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Residues in contact with GLY 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.5 33.4 - - - +
100D LEU* 2.7 40.5 + - - -
136D PRO 3.1 0.4 - - - -
137D LEU* 1.3 76.1 - - - +
139D GLU* 1.3 61.3 + - - +
140D TYR 3.1 1.5 + - - -
141D GLY* 3.4 10.8 + - - -
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Residues in contact with GLU 139 (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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39D HIS* 5.1 8.0 + - - +
40D ALA* 5.1 9.7 + - - +
41D PHE* 3.8 8.6 - - - -
129D LYS* 5.7 1.0 - - - -
135D LEU* 4.1 23.4 - - + +
136D PRO* 3.0 34.1 + - + +
137D LEU 3.0 0.2 - - - -
138D GLY* 1.3 77.8 - - - +
140D TYR* 1.3 77.2 + - + +
141D GLY 3.6 0.2 - - - -
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Residues in contact with TYR 140 (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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104D VAL* 3.9 14.1 - - + -
126D PHE* 3.6 24.5 - - + -
127D GLU* 4.9 1.0 - - - +
129D LYS* 3.7 32.8 + - + +
130D PRO 3.7 11.6 + - - -
131D LEU* 3.4 38.0 - - + -
132D GLU* 2.8 29.7 + - - +
135D LEU* 3.5 18.9 - - + +
136D PRO 3.8 16.4 - - - -
137D LEU* 3.1 12.1 + - - +
138D GLY 3.1 0.8 - - - -
139D GLU* 1.3 95.1 - - + +
141D GLY* 1.3 64.5 + - - +
142D LEU* 3.2 7.5 + - + -
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Residues in contact with GLY 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU* 5.7 0.7 - - - -
126D PHE* 4.6 4.7 - - - -
138D GLY* 3.4 12.9 + - - -
139D GLU 3.6 1.0 + - - -
140D TYR* 1.3 79.4 - - - +
142D LEU* 1.3 66.6 + - - +
143D LYS* 3.4 19.6 + - - +
146D SER* 4.9 0.2 + - - -
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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