Contacts of the helix formed by residues 136 - 145 (chain F) in PDB entry 6G2T
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 GLN 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ASP* 4.3 3.4 + - - -
11F ASN 4.3 3.0 + - - -
12F GLY* 4.3 19.8 - - - -
105F THR* 3.1 39.7 + - + +
106F GLU 2.7 20.0 + - - +
107F ALA* 3.6 25.1 - - - +
108F PRO* 4.9 2.5 - - + +
135F ILE* 1.3 73.2 - - - +
137F ALA* 1.3 62.3 + - - +
139F LEU* 3.4 2.6 + - - +
140F SER* 3.3 17.8 + - - -
153F ASP* 3.3 24.2 - - - +
158F VAL 5.6 0.2 - - - +
160F HIS* 4.4 6.6 + - - -
338F VAL* 3.7 20.0 - - + +
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PRO* 5.0 2.7 - - + +
135F ILE* 3.3 5.3 - - + +
136F GLN* 1.3 78.6 - - - +
138F VAL* 1.3 59.8 + - - +
140F SER* 2.7 23.2 + - - -
141F LEU* 3.4 4.3 + - - +
151F VAL* 3.7 29.0 - - + +
153F ASP* 3.9 8.4 + - + +
160F HIS* 5.9 0.4 - - + +
162F VAL* 3.4 43.5 - - + +
164F ILE* 5.7 1.1 - - + -
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.8 21.8 - - + +
43D MET* 3.4 17.3 - - - -
134F ALA* 6.3 0.2 - - + -
135F ILE* 3.3 28.7 + - + +
136F GLN 3.3 0.8 - - - -
137F ALA* 1.3 76.1 - - + +
139F LEU* 1.3 69.3 + - + +
141F LEU* 3.1 16.6 + - - +
142F TYR* 3.1 42.5 + - + -
162F VAL* 5.4 1.3 - - + -
164F ILE* 4.2 24.2 - - + -
345F LEU* 6.2 0.7 - - + -
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 5.4 2.9 - - + -
103F LEU* 4.5 10.1 - - + -
105F THR* 4.2 17.7 - - - +
134F ALA* 3.4 26.5 - - + +
135F ILE 2.9 28.0 - - - +
136F GLN 3.4 6.0 + - - +
138F VAL* 1.3 77.3 - - + +
140F SER* 1.3 66.8 + - - +
142F TYR* 3.1 11.8 + - + -
143F ALA 3.2 2.1 + - - -
337F SER 4.1 0.9 - - - -
338F VAL* 3.3 21.1 - - + +
339F TRP* 5.5 0.2 - - - -
341F GLY* 2.9 27.8 + - - +
342F GLY* 3.4 32.1 - - - +
345F LEU* 4.5 8.7 - - + -
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Residues in contact with SER 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLN 3.3 9.9 + - - -
137F ALA 2.7 21.5 + - - -
139F LEU* 1.3 79.1 - - - +
141F LEU* 1.3 62.0 + - - +
143F ALA* 3.2 5.7 + - - +
144F SER* 3.2 23.1 + - - -
151F VAL* 3.2 19.8 - - - +
297F VAL* 5.0 4.5 - - - +
299F SER* 3.8 26.5 - - - -
337F SER* 3.9 17.7 - - - -
338F VAL* 4.0 8.6 - - - +
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D MET* 4.1 22.9 - - + -
137F ALA 3.8 8.3 - - - +
138F VAL* 3.1 10.9 + - - +
140F SER* 1.3 84.0 + - - +
142F TYR* 1.3 56.6 + - - +
144F SER* 3.2 9.6 + - - -
145F GLY 3.0 21.7 + - - -
146F ARG* 3.0 44.8 + - + +
147F THR 4.5 3.1 - - - +
148F THR 4.6 12.3 - - - +
149F GLY* 4.9 1.6 - - - +
151F VAL* 4.4 16.6 - - + -
164F ILE* 3.7 36.3 - - + -
297F VAL* 4.9 10.1 - - + -
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Residues in contact with TYR 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D MET* 3.4 23.8 - - + +
44D VAL* 2.7 45.3 + - + +
138F VAL* 3.1 50.6 + - + -
139F LEU* 3.1 12.6 + - + +
141F LEU* 1.3 73.5 - - - +
143F ALA* 1.3 65.1 + - - +
145F GLY* 3.1 15.3 + - - +
146F ARG 5.5 0.2 - - - -
341F GLY* 3.8 5.2 - - - -
344F ILE* 3.5 47.3 - - + +
345F LEU* 4.1 24.6 - - + +
348F LEU* 5.3 7.9 - - + -
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Residues in contact with ALA 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LEU 3.2 3.8 + - - -
140F SER 3.2 7.4 + - - +
142F TYR* 1.3 78.5 - - - +
144F SER* 1.3 62.5 + - - +
145F GLY* 3.5 0.7 + - - -
337F SER* 3.3 39.0 - - - +
340F ILE* 3.7 28.4 - - + +
341F GLY* 4.1 1.7 - - - +
344F ILE* 5.3 0.9 - - - -
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Residues in contact with SER 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F SER 3.2 10.1 + - - -
141F LEU* 3.2 14.1 - - - -
143F ALA* 1.3 79.5 - - - +
145F GLY* 1.3 60.1 + - - +
146F ARG* 3.3 29.3 - - - +
297F VAL* 3.8 21.2 - - - +
329F ILE* 5.7 1.5 - - - +
331F PRO* 5.0 11.9 - - - +
337F SER* 5.6 1.4 + - - -
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F LEU 3.0 5.8 + - - -
142F TYR* 3.1 14.1 + - - -
143F ALA 4.5 0.4 - - - -
144F SER* 1.3 77.3 - - - +
146F ARG* 1.3 60.8 + - - +
147F THR* 4.2 4.1 + - - +
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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