Contacts of the helix formed by residues 142 - 150 (chain B) in PDB entry 4GDY
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 TYR 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 5.6 2.7 - - + -
293A LEU* 4.6 8.0 - - - +
118B GLN* 3.2 28.9 + - - -
121B LEU* 5.4 0.9 - - + -
141B ALA* 1.4 72.0 - - - +
143B SER* 1.3 64.9 + - - +
144B GLY* 3.6 21.1 - - - -
145B THR* 3.0 50.4 + - + +
146B LEU* 3.4 10.4 + - - +
195B TYR* 4.4 4.5 + - - +
197B VAL* 5.1 3.1 - - + +
201B ASN* 5.0 1.2 + - - -
202B ASN* 3.2 34.6 + - + -
230B ASP* 4.6 0.2 - - - -
387B PHE* 4.9 1.1 - + - -
501B 0X1 3.4 81.1 + + + -
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Residues in contact with SER 143 (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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17A SER* 4.7 1.2 + - - -
18A PRO* 4.2 19.5 - - - +
19A ILE* 3.3 27.9 - - - +
141B ALA 3.3 4.6 + - - -
142B TYR* 1.3 75.3 - - - +
144B GLY* 1.3 54.8 + - - +
146B LEU* 3.2 7.6 + - - +
147B GLN* 2.8 41.1 + - - +
386B ALA* 3.6 26.5 - - - -
387B PHE* 4.4 9.9 - - - -
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Residues in contact with GLY 144 (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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290A VAL* 4.5 4.7 - - - +
118B GLN* 4.1 8.4 + - - -
142B TYR* 3.2 30.1 - - - -
143B SER* 1.3 80.9 + - - +
145B THR* 1.4 61.7 + - - +
147B GLN* 3.7 5.6 + - - +
148B SER* 3.2 25.3 + - - -
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Residues in contact with THR 145 (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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118B GLN* 5.4 2.0 - - - +
121B LEU* 5.5 3.4 - - + -
125B PHE* 4.0 21.1 - - - -
137B LEU* 4.1 11.3 - - - +
141B ALA* 5.5 0.3 - - - +
142B TYR* 3.0 29.6 + - + +
144B GLY* 1.4 72.1 - - - +
146B LEU* 1.3 60.6 + - - +
148B SER* 3.2 6.8 + - - -
149B LEU* 2.9 34.8 + - - +
195B TYR* 3.0 47.7 - - + +
230B ASP* 4.7 0.7 - - - +
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Residues in contact with LEU 146 (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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137B LEU* 4.0 27.1 - - + -
139B GLU* 5.5 0.9 - - + -
141B ALA* 3.8 17.5 - - + +
142B TYR 3.4 10.0 + - - +
143B SER* 3.2 6.4 + - - +
145B THR* 1.3 76.4 + - - +
147B GLN* 1.3 60.7 + - + +
149B LEU* 3.3 4.7 + - - +
150B HIS* 3.0 33.7 + - - +
156B ILE* 4.6 6.5 - - + +
386B ALA 3.9 11.0 - - - +
387B PHE 3.6 33.0 - - - +
388B TYR 3.8 11.4 - - - +
389B VAL* 3.9 28.9 - - + +
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Residues in contact with GLN 147 (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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14A ARG* 5.3 2.4 + - - +
15A ASN* 3.0 55.7 + - - +
16A PRO 4.1 5.7 + - - +
17A SER* 5.1 4.0 - - - +
18A PRO* 4.7 18.0 - - + +
290A VAL* 4.1 19.7 - - + +
143B SER* 2.8 21.6 + - - +
144B GLY* 4.0 6.1 - - - +
146B LEU* 1.3 79.1 - - + +
148B SER* 1.4 55.9 + - - +
150B HIS* 4.5 8.5 + - - +
151B PRO* 3.3 22.5 - - - +
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Residues in contact with SER 148 (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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14A ARG* 5.2 2.6 + - - -
290A VAL* 3.3 34.0 + - - +
118B GLN* 3.8 6.2 + - - -
122B CYS* 4.9 4.6 - - - +
125B PHE* 4.0 21.0 - - - -
144B GLY 3.2 15.3 + - - -
145B THR* 3.3 10.8 - - - -
147B GLN* 1.4 77.2 - - - +
149B LEU* 1.4 61.8 + - - +
151B PRO* 3.3 11.3 - - - +
152B LEU* 3.5 16.4 - - - +
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Residues in contact with LEU 149 (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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125B PHE* 3.6 30.5 - - + -
129B ILE* 3.6 30.7 - - + -
135B VAL* 4.4 9.9 - - + -
137B LEU* 4.1 21.8 - - + -
145B THR* 2.9 24.6 + - - +
146B LEU* 3.3 2.2 + - - +
148B SER* 1.4 75.4 - - - +
150B HIS* 1.3 63.3 + - - +
152B LEU* 3.0 23.4 + - + +
153B GLY 3.9 0.7 + - - -
154B CYS* 3.8 17.8 + - - +
156B ILE* 4.0 28.0 - - + -
193B PHE* 4.4 6.5 - - + -
195B TYR* 5.9 0.2 - - + -
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Residues in contact with HIS 150 (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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13A ALA* 3.3 39.0 + - + +
14A ARG* 5.2 0.6 - - - -
15A ASN* 3.6 18.4 + - - -
146B LEU 3.0 18.0 + - - +
147B GLN* 4.5 9.4 + - - +
149B LEU* 1.3 74.7 - - - +
151B PRO* 1.4 69.5 - - + +
152B LEU 3.3 1.0 + - - -
153B GLY* 3.5 10.7 + - - -
156B ILE* 5.3 3.5 - - - +
389B VAL* 6.5 1.1 - - + -
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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