Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 1GNG
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 THR 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL 5.2 0.4 - - - +
136A PRO 3.9 8.4 + - - +
137A GLU* 1.3 82.2 + - - +
139A VAL* 1.3 64.4 + - - +
140A TYR* 2.8 12.0 + - - +
141A ARG* 3.0 35.1 + - + +
142A VAL* 3.1 13.9 + - - +
184A PRO 3.9 6.5 - - - -
185A GLN* 3.6 19.5 - - - +
187A LEU 3.1 11.0 - - - +
188A LEU* 4.1 12.8 - - + -
189A LEU* 3.3 6.3 - - - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A THR* 1.3 71.1 - - - +
140A TYR* 1.3 56.2 + - - +
142A VAL* 3.9 3.0 - - + +
143A ALA* 3.0 27.4 + - - +
153A LEU* 5.7 0.4 - - + -
161A TYR* 4.1 17.9 - - + -
184A PRO* 3.7 14.8 + - + +
187A LEU* 2.8 35.9 + - + -
189A LEU* 3.1 33.8 - - + +
196A LEU* 4.0 12.1 - - + -
246A VAL* 4.9 2.7 - - + -
250A LEU* 4.1 27.8 - - + -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A THR* 2.8 10.5 - - - +
139A VAL* 1.3 76.3 - - - +
141A ARG* 1.3 69.1 + - + +
143A ALA* 3.3 4.3 + - + +
144A ARG* 2.8 71.3 + - + +
184A PRO* 3.2 34.2 + - + +
185A GLN* 3.7 37.0 - - + +
249A GLU* 4.9 9.4 - - - -
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO 3.7 19.7 + - - -
137A GLU* 3.4 24.2 - - - +
138A THR* 3.0 16.2 + - - +
140A TYR* 1.3 85.3 - - + +
142A VAL* 1.3 52.9 + - - +
144A ARG* 3.2 36.0 + - - +
145A HIS* 2.7 34.9 + - - +
148A ARG* 5.6 0.4 - - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 3.5 25.1 - - + +
138A THR 3.1 14.1 + - - +
139A VAL* 3.9 4.0 - - + +
141A ARG* 1.3 75.4 - - - +
143A ALA* 1.3 59.4 + - - +
145A HIS* 2.8 30.2 + - - +
146A TYR* 3.1 30.9 + - + -
153A LEU* 4.1 16.2 - - + -
161A TYR* 4.6 14.6 - - + +
189A LEU* 3.5 20.4 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL* 3.0 18.5 + - + +
140A TYR* 3.6 5.6 - - + +
142A VAL* 1.3 80.7 - - - +
144A ARG* 1.3 63.8 + - - +
145A HIS 3.2 0.3 + - - -
146A TYR* 3.3 7.3 + - - +
147A SER* 3.0 23.8 + - - -
153A LEU* 5.6 5.2 - - - -
184A PRO* 5.9 2.0 - - + -
249A GLU* 5.6 8.1 - - + +
250A LEU* 3.9 25.8 - - + -
253A GLY* 5.4 0.7 - - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 2.8 55.3 + - + +
141A ARG* 3.5 48.8 + - - +
143A ALA* 1.3 72.7 - - - +
145A HIS* 1.3 63.2 + - - +
147A SER* 3.6 8.2 - - - -
148A ARG* 3.0 74.9 + - + +
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG 2.7 13.6 + - - +
142A VAL* 2.8 18.3 + - - +
144A ARG* 1.3 79.8 - - - +
146A TYR* 1.3 81.2 + + - -
148A ARG* 3.2 9.1 + - - +
149A ALA* 3.1 26.9 + - + +
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.1 26.4 + - + -
143A ALA* 3.9 5.8 - - - +
145A HIS* 1.3 95.1 - + - +
147A SER* 1.3 63.5 + - - +
149A ALA* 2.9 17.1 + - - +
150A LYS 3.0 9.2 + - - -
151A GLN* 3.0 42.8 + - + +
152A THR 3.5 19.7 - - - -
153A LEU* 3.8 27.3 - - + +
154A PRO* 3.4 32.2 - - + +
157A TYR* 4.8 8.5 - - - -
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA 3.0 17.5 + - - -
144A ARG* 3.6 11.4 - - - -
146A TYR* 1.3 78.6 - - - +
148A ARG* 1.3 58.7 + - - +
150A LYS* 3.0 22.0 + - - +
151A GLN 4.2 4.5 - - - -
253A GLY* 3.2 29.2 + - - -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 5.6 0.4 - - - +
144A ARG* 3.0 80.9 + - + +
145A HIS* 3.7 7.2 - - - +
147A SER* 1.3 72.4 - - - +
149A ALA* 1.3 58.0 + - - +
150A LYS* 3.0 15.8 + - - +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS* 3.1 19.8 + - + +
146A TYR* 2.9 11.5 + - - +
148A ARG* 1.3 74.6 - - - +
150A LYS* 1.3 62.4 + - - +
151A GLN* 2.9 34.7 + - + +
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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