Contacts of the helix formed by residues 135 - 143 (chain B) in PDB entry 6CQT
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B TRP* 3.6 30.5 - - - -
133B TYR 3.1 8.9 + - - -
134B ASP* 1.3 73.1 + - - +
136B ARG* 1.3 62.6 + - - +
137B PHE 3.3 1.7 + - - -
138B LEU* 3.5 5.4 + - - +
139B VAL* 3.2 27.2 + - - +
146B LEU* 4.2 11.7 - - - -
455B PHE* 4.3 7.2 - - - -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.8 35.8 - - + +
23B LYS* 2.9 31.7 + - - +
24B THR* 3.6 10.6 - - + +
29B VAL* 3.5 26.1 - - + +
102B TRP* 3.9 10.8 - - + -
134B ASP* 2.7 31.0 + - - +
135B GLY* 1.3 78.1 - - - +
137B PHE* 1.3 85.5 + - + +
139B VAL* 4.7 1.1 - - - -
140B GLN* 3.1 29.6 + - - +
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.4 4.5 - - - -
25B PRO* 3.8 28.5 - - + -
134B ASP* 4.2 11.2 - - - -
135B GLY 3.3 0.6 - - - -
136B ARG* 1.3 100.4 - - + +
138B LEU* 1.3 60.6 + - - +
140B GLN* 4.0 3.5 - - - +
141B ALA* 2.9 34.1 + - - +
455B PHE 3.5 21.8 - - - +
456B GLY* 3.6 21.1 - - - +
457B ILE* 4.1 21.8 - - + -
459B LEU* 4.0 17.2 - - + +
460B ASP* 3.9 35.0 - - + -
461B PRO* 5.6 0.2 - - + -
477B MET* 4.0 2.6 - - - +
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Residues in contact with LEU 138 (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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115B LEU* 4.4 19.5 - - + -
135B GLY* 3.5 8.9 + - - +
136B ARG 3.5 0.4 - - - -
137B PHE* 1.3 77.6 - - - +
139B VAL* 1.3 59.7 + - + +
142B GLU* 2.9 41.4 + - + +
143B ARG 3.8 0.2 + - - -
144B THR* 4.0 5.3 + - - +
146B LEU* 4.2 24.5 - - + -
200B PHE* 4.4 13.5 - - + -
454B ILE* 3.6 22.7 - - + +
455B PHE* 4.2 16.4 + - + +
477B MET* 3.8 40.8 - - + +
480B TRP* 5.5 4.3 - - + -
481B ALA* 5.1 1.6 - - + -
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Residues in contact with VAL 139 (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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29B VAL* 4.2 9.0 - - + -
102B TRP* 3.6 25.1 - - + +
103B THR* 3.3 37.5 - - - +
104B PRO* 3.4 9.4 - - + +
135B GLY 3.2 17.5 + - - +
136B ARG* 4.0 2.5 - - - +
138B LEU* 1.3 80.2 - - + +
140B GLN* 1.3 58.2 + - - +
143B ARG* 3.0 26.5 + - - -
144B THR* 3.3 24.7 - - - +
146B LEU* 3.7 17.5 - - + -
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Residues in contact with GLN 140 (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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24B THR* 3.6 18.6 + - + +
26B GLY* 3.2 38.0 + - - +
27B GLY 4.0 6.5 - - - +
28B PRO 4.6 2.9 - - - +
29B VAL* 3.6 14.1 - - + -
104B PRO* 5.8 2.0 - - - -
136B ARG 3.1 19.4 + - - +
137B PHE* 4.0 3.0 - - - +
139B VAL* 1.3 81.6 - - - +
141B ALA* 1.3 71.7 + - - +
143B ARG* 4.0 12.9 + - - +
459B LEU* 6.1 0.9 - - - +
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Residues in contact with ALA 141 (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 PHE 2.9 19.0 + - - +
138B LEU 4.3 0.7 - - - +
140B GLN* 1.3 89.0 - - - +
142B GLU* 1.3 72.0 + - + +
143B ARG* 3.6 3.2 - - - +
459B LEU* 5.2 4.0 - - + -
474B GLN* 6.0 2.7 - - + +
477B MET* 3.7 25.6 - - + -
478B ARG* 5.3 3.1 + - - -
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Residues in contact with GLU 142 (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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138B LEU* 2.9 17.9 + - + +
141B ALA* 1.3 87.1 - - + +
143B ARG* 1.3 72.6 + - - +
144B THR* 3.4 5.1 - - + +
474B GLN 4.5 2.9 - - - +
477B MET* 3.5 30.8 - - + +
478B ARG* 2.8 45.9 + - - +
481B ALA* 3.5 14.6 - - + -
485B ARG* 3.0 45.0 + - - -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 3.8 33.9 - - + +
105B TYR 5.3 4.8 + - - -
106B PRO* 5.1 6.7 + - - +
108B PRO* 5.3 9.7 - - - +
112B THR* 3.1 18.2 - - + +
113B PRO* 4.3 5.5 - - - +
138B LEU 3.8 0.4 + - - -
139B VAL 3.0 15.9 + - - +
140B GLN* 4.0 14.6 + - - +
141B ALA 4.8 2.2 - - - +
142B GLU* 1.3 82.1 - - - +
144B THR* 1.3 61.2 + - - +
485B ARG* 5.0 0.5 + - - -
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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