Contacts of the helix formed by residues 135 - 141 (chain D) in PDB entry 1C2O
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 GLY 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.4 25.6 - - - +
133D TYR 3.0 9.2 + - - -
134D ASP* 1.3 69.3 + - - +
136D ARG* 1.3 62.0 + - - +
137D PHE 3.5 0.4 - - - -
138D LEU 4.3 2.7 - - - -
139D ALA* 3.4 22.2 + - - +
146D LEU* 3.4 33.1 - - - +
455D PHE* 4.2 2.7 - - - -
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Residues in contact with ARG 136 (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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22D LEU* 3.4 35.6 - - + +
23D LYS 3.9 24.5 + - - +
24D ALA* 3.8 19.0 - - + +
25D PRO* 5.2 0.8 - - - +
29D VAL* 4.0 14.6 - - + +
102D TRP* 3.3 18.4 - - + -
134D ASP* 3.0 42.7 + - - +
135D GLY* 1.3 73.3 - - - +
137D PHE* 1.3 81.9 + - + +
139D ALA* 3.1 2.8 + - - +
140D GLN* 2.6 38.3 + - - +
460D ASP* 5.8 1.8 + - - -
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Residues in contact with PHE 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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24D ALA* 4.8 1.1 - - + -
25D PRO* 3.6 35.7 - - + -
134D ASP* 3.8 15.9 - - - -
135D GLY 3.5 0.2 - - - -
136D ARG* 1.3 99.2 - - + +
138D LEU* 1.3 58.7 + - - +
139D ALA 2.9 0.2 + - - -
140D GLN* 4.2 5.2 - - - -
141D VAL* 2.7 39.4 + - + +
455D PHE 3.5 20.9 - - - +
456D GLY* 3.7 18.2 - - - +
457D LEU* 3.9 22.4 - - + -
459D LEU* 4.1 10.8 - - + -
460D ASP* 4.0 28.5 - - + -
463D LEU* 5.3 0.9 - - + -
477D MET* 3.8 11.7 - - + -
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Residues in contact with LEU 138 (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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115D LEU* 4.5 11.2 - - + -
135D GLY* 3.8 1.4 + - - -
136D ARG 3.5 0.6 - - - -
137D PHE* 1.3 74.9 - - - +
139D ALA* 1.3 58.3 + - - +
142D GLU* 3.5 12.3 + - - +
144D ALA* 3.2 26.6 + - + +
146D LEU* 3.9 22.7 - - + -
200D PHE* 5.0 5.8 - - + -
454D ILE* 3.5 11.7 - - + +
455D PHE* 3.5 51.5 + - + +
477D MET* 3.2 40.6 - - + +
480D TRP* 5.2 5.8 - - + -
481D THR* 4.3 17.9 - - + -
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Residues in contact with ALA 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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29D VAL* 4.0 17.0 - - + -
102D TRP* 4.2 14.1 - - + -
104D PRO* 3.9 12.3 - - - +
135D GLY 3.4 12.8 + - - +
136D ARG 3.1 7.1 + - - +
138D LEU* 1.3 75.8 - - - +
140D GLN* 1.3 71.5 + - - +
143D GLY* 2.8 24.4 + - - -
144D ALA 2.9 24.7 - - - +
146D LEU* 5.1 1.3 - - + +
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Residues in contact with GLN 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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24D ALA* 3.3 27.2 - - + +
25D PRO* 5.5 0.2 - - - +
26D GLY* 3.1 44.4 + - - -
27D GLY* 3.8 14.5 - - - +
28D PRO* 4.4 7.7 + - - +
29D VAL* 4.2 7.6 - - + +
104D PRO* 5.0 7.2 - - - +
136D ARG 2.6 22.7 + - - +
137D PHE* 3.7 3.2 - - - +
139D ALA* 1.3 79.6 - - - +
141D VAL* 1.3 83.3 + - - +
143D GLY* 3.8 2.9 + - - -
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Residues in contact with VAL 141 (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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26D GLY* 5.7 0.4 - - - +
137D PHE* 2.7 23.5 + - + +
140D GLN* 1.3 94.9 - - + +
142D GLU* 1.3 85.6 + - + +
143D GLY 3.2 1.8 + - - -
459D LEU* 3.5 33.2 - - + -
474D GLN* 5.7 7.2 - - + +
477D MET* 4.6 6.5 - - + -
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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