Contacts of the helix formed by residues 122 - 133 (chain B) in PDB entry 3GUU
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 ASP 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B TYR* 4.7 1.8 + - - -
93B TYR* 2.7 32.1 + - - -
121B LEU* 1.3 78.7 - - - +
123B THR* 1.3 68.9 + - - +
124B PRO 3.4 0.2 - - - -
125B ILE* 3.2 8.6 + - - +
126B ILE* 3.1 34.1 + - + +
183B TYR* 5.1 4.0 - - - +
370B GLU* 2.6 32.4 - - - +
371B ILE* 4.9 3.6 - - + -
374B LEU* 3.6 23.3 - - + +
424B LEU* 3.8 14.8 - - + +
435B PHE* 4.5 4.3 - - + -
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Residues in contact with THR 123 (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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46B ILE* 4.2 2.9 - - + -
90B TYR* 3.0 37.5 + - + -
92B VAL* 4.9 0.6 - - + +
93B TYR* 4.4 2.4 + - - -
107B TYR* 3.6 32.1 - - + +
118B THR 2.8 23.2 + - - +
119B ALA* 3.6 12.1 - - - +
120B VAL 3.7 4.1 + - - -
122B ASP* 1.3 80.8 + - - +
124B PRO* 1.3 68.2 - - - +
126B ILE* 3.2 3.4 + - - +
127B ILE* 3.1 29.2 + - + +
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Residues in contact with PRO 124 (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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46B ILE* 3.8 30.2 - - + +
50B ASN* 4.9 2.3 + - - -
119B ALA 3.3 8.1 - - - +
120B VAL* 3.1 32.1 - - + +
121B LEU 3.4 12.3 - - - +
123B THR* 1.3 86.7 - - - +
125B ILE* 1.3 61.8 + - + +
127B ILE 4.6 0.2 - - - +
128B GLY* 2.9 27.5 + - - -
417B LEU* 4.5 3.0 - - - +
420B GLN* 5.6 3.6 - - - +
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Residues in contact with ILE 125 (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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121B LEU 3.9 17.3 - - - +
122B ASP* 3.2 8.9 + - - +
124B PRO* 1.3 80.7 - - + +
126B ILE* 1.3 56.2 + - - +
129B TRP* 3.0 28.2 + - - +
374B LEU* 4.5 15.9 - - + -
413B LEU* 4.4 19.1 - - + -
417B LEU* 4.1 24.5 - - + +
420B GLN* 3.7 26.2 - - + +
421B LEU* 3.5 37.0 - - + +
424B LEU* 4.2 9.9 - - + -
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Residues in contact with ILE 126 (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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88B PHE* 3.5 31.4 - - + -
90B TYR* 3.7 31.4 - - + +
122B ASP* 3.1 31.0 + - - +
123B THR 3.2 5.1 + - - +
125B ILE* 1.3 73.9 - - - +
127B ILE* 1.3 60.6 + - - +
129B TRP* 3.4 5.9 + - - +
130B ALA* 3.0 26.7 + - - +
181B GLU* 3.9 12.3 - - - +
374B LEU* 3.8 26.7 - - + -
378B LEU* 3.9 26.5 - - + -
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Residues in contact with ILE 127 (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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46B ILE* 3.7 36.1 - - + -
76B TRP* 4.2 11.4 - - + -
88B PHE* 4.3 3.6 - - + -
90B TYR* 3.4 44.2 - - + -
107B TYR* 4.9 4.7 - - + +
123B THR* 3.1 19.6 + - + +
126B ILE* 1.3 72.8 - - - +
128B GLY* 1.3 61.2 + - - +
130B ALA* 3.1 6.3 + - - +
131B LEU* 2.8 33.6 + - + +
137B VAL* 3.6 30.7 - - + -
139B SER* 5.6 0.2 - - - -
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Residues in contact with GLY 128 (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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46B ILE* 4.5 0.4 - - - +
50B ASN* 3.6 29.9 - - - +
124B PRO 2.9 20.0 + - - -
125B ILE 4.1 0.2 - - - -
127B ILE* 1.3 72.4 - - - +
129B TRP* 1.3 65.4 + - - +
131B LEU* 3.2 3.8 + - - +
132B GLN* 2.9 27.5 + - - +
417B LEU* 3.9 10.3 - - - -
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Residues in contact with TRP 129 (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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88B PHE* 4.5 3.4 - + - -
125B ILE 3.0 19.4 + - - +
126B ILE 3.5 8.7 - - - +
128B GLY* 1.3 73.9 - - - +
130B ALA* 1.3 85.4 + - + +
132B GLN* 3.2 3.9 + - + +
133B GLN* 3.1 59.6 + - + +
135B TYR* 3.7 26.9 - + - -
378B LEU* 3.2 61.9 - - + -
381B ILE* 4.2 9.9 - - + -
382B LYS* 4.0 19.0 - - + +
412B VAL* 3.2 29.9 + - + +
413B LEU* 3.7 22.0 - - + -
417B LEU* 3.4 15.2 - - + +
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Residues in contact with ALA 130 (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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88B PHE* 3.6 32.1 - - + -
126B ILE 3.0 15.1 + - - +
127B ILE 3.1 7.6 + - - +
129B TRP* 1.3 89.1 - - + +
131B LEU* 1.3 62.6 + - - +
133B GLN* 3.1 14.3 + - - +
135B TYR* 3.1 28.8 + - + -
137B VAL* 3.7 9.9 - - + -
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Residues in contact with LEU 131 (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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46B ILE* 3.9 21.3 - - + -
50B ASN* 3.9 24.2 - - + +
52B ALA* 3.9 22.4 - - + -
76B TRP* 3.6 32.5 - - + +
78B PRO* 3.9 22.6 - - + +
80B LYS 5.1 0.2 - - - +
127B ILE* 2.8 23.7 + - + +
128B GLY 3.7 4.0 - - - +
130B ALA* 1.3 72.4 - - - +
132B GLN* 1.3 58.9 + - - +
134B GLY* 2.9 20.1 + - - -
135B TYR 3.6 18.6 - - - +
137B VAL* 3.9 9.2 - - + -
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Residues in contact with GLN 132 (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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49B ALA 5.2 0.8 + - - -
50B ASN* 2.8 43.1 + - - +
128B GLY 2.9 21.0 + - - +
129B TRP* 3.2 7.2 + - + +
131B LEU* 1.3 75.8 - - - +
133B GLN* 1.3 67.7 + - - +
134B GLY 3.2 0.2 - - - -
413B LEU 5.8 1.8 - - - +
417B LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 133 (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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82B ALA* 3.6 16.1 - - - +
129B TRP* 3.1 57.7 + - + +
130B ALA 3.1 8.9 + - - +
132B GLN* 1.3 84.6 + - - +
134B GLY* 1.3 59.1 + - - +
135B TYR* 3.4 35.5 - - + +
382B LYS* 3.7 21.7 + - - +
412B VAL 4.4 3.8 + - - -
413B LEU 5.9 0.2 + - - -
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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