Contacts of the helix formed by residues 121 - 133 (chain A) 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 LEU 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A TYR* 5.0 4.0 - - - +
117A VAL* 3.9 31.2 - - + +
120A VAL* 1.3 87.1 - - + +
122A ASP* 1.3 65.7 + - - +
124A PRO* 3.4 14.3 - - - +
125A ILE* 3.8 13.7 - - - +
424A LEU* 3.9 24.9 - - + +
427A LYS* 5.7 5.2 - - + -
428A GLN 3.9 16.6 - - - +
430A ALA 4.0 11.4 - - - +
435A PHE* 3.9 27.8 - - + -
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Residues in contact with ASP 122 (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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90A TYR* 4.7 1.4 + - - -
93A TYR* 2.8 29.1 + - - -
121A LEU* 1.3 79.2 - - - +
123A THR* 1.3 69.8 + - - +
125A ILE* 3.1 15.9 + - - +
126A ILE* 3.2 26.9 + - + +
183A TYR* 5.3 2.9 - - - +
370A GLU* 2.3 35.0 - - - +
371A ILE* 4.9 2.9 - - + -
374A LEU* 4.0 21.6 - - + +
424A LEU* 3.8 16.1 - - + +
435A PHE* 4.7 4.4 - - - -
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.3 1.3 - - + -
90A TYR* 2.8 43.7 + - + -
92A VAL* 4.6 0.2 - - + -
93A TYR* 4.5 2.8 + - - -
107A TYR* 3.8 24.0 - - + +
118A THR 3.0 21.7 + - - +
119A ALA* 3.8 16.6 - - - +
120A VAL 3.6 1.2 + - - -
122A ASP* 1.3 81.7 + - - +
124A PRO* 1.4 70.0 - - - +
126A ILE* 3.3 3.2 + - - +
127A ILE* 3.0 29.3 + - + +
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Residues in contact with PRO 124 (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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46A ILE* 3.9 28.2 - - + +
50A ASN* 5.0 1.2 + - - -
119A ALA 3.2 10.5 - - - +
120A VAL* 3.2 34.1 - - + +
121A LEU 3.4 14.8 - - - +
123A THR* 1.4 84.7 - - - +
125A ILE* 1.3 55.6 + - + +
128A GLY* 2.8 28.8 + - - +
417A LEU* 4.7 2.1 - - - +
420A GLN* 5.3 4.7 - - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU 3.8 16.8 - - - +
122A ASP* 3.1 8.8 + - - +
124A PRO* 1.3 79.5 - - + +
126A ILE* 1.3 54.1 + - + +
128A GLY 3.8 0.2 - - - -
129A TRP* 2.8 35.6 + - - +
374A LEU* 4.8 12.8 - - + -
413A LEU* 4.8 10.3 - - + -
417A LEU* 3.9 32.2 - - + +
420A GLN* 3.6 26.2 - - + +
421A LEU* 3.6 41.3 - - + +
424A LEU* 4.1 13.2 - - + -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.7 20.4 - - + -
90A TYR* 3.7 31.6 - - + +
122A ASP* 3.2 25.8 + - + +
123A THR 3.3 6.0 + - - +
125A ILE* 1.3 73.4 - - - +
127A ILE* 1.3 61.5 + - - +
129A TRP* 3.6 6.1 + - - +
130A ALA* 3.1 27.2 + - - +
181A GLU* 3.6 27.4 - - - +
183A TYR* 6.4 1.8 - - + -
374A LEU* 4.0 30.7 - - + -
378A LEU* 4.2 18.4 - - + -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.7 41.5 - - + -
76A TRP* 4.0 15.9 - - + -
88A PHE* 5.1 0.9 - - + -
90A TYR* 3.9 21.5 - - + -
107A TYR* 3.7 27.6 - - + +
123A THR* 3.0 21.9 + - + +
126A ILE* 1.3 71.8 - - - +
128A GLY* 1.3 68.1 + - - +
130A ALA* 3.2 7.3 + - - +
131A LEU* 2.9 31.2 + - + +
137A VAL* 3.8 26.7 - - + -
139A SER* 5.0 0.2 - - - -
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Residues in contact with GLY 128 (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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46A ILE* 4.6 0.6 - - - +
50A ASN* 3.6 28.6 - - - +
124A PRO 2.8 20.8 + - - -
127A ILE* 1.3 78.0 - - - +
129A TRP* 1.3 60.5 + - - -
131A LEU* 3.3 2.9 + - - +
132A GLN* 2.9 27.2 + - - +
417A LEU* 4.1 9.6 - - - -
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Residues in contact with TRP 129 (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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88A PHE* 4.3 9.2 - + - -
125A ILE 2.8 23.0 + - - +
126A ILE 3.7 5.4 - - - +
127A ILE 3.3 0.2 - - - -
128A GLY* 1.3 73.4 - - - +
130A ALA* 1.3 77.5 + - + +
132A GLN* 3.2 2.2 + - - -
133A GLN* 3.0 69.2 + - + +
135A TYR* 3.8 19.3 - + - -
378A LEU* 3.1 67.8 - - + -
381A ILE* 4.4 1.8 - - + -
382A LYS* 4.0 23.8 - - + -
412A VAL* 3.0 30.3 + - + -
413A LEU* 3.8 28.1 - - + +
417A LEU* 3.6 13.7 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.8 36.3 - - + -
126A ILE 3.1 17.6 + - - +
127A ILE 3.2 4.7 + - - +
129A TRP* 1.3 84.2 - - + +
131A LEU* 1.3 60.0 + - - +
133A GLN* 3.2 7.0 + - - -
135A TYR* 2.9 40.5 + - + +
137A VAL* 3.8 8.1 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.0 20.9 - - + +
50A ASN* 3.9 23.1 - - + +
52A ALA* 3.8 21.3 - - + -
76A TRP* 3.8 29.4 - - + +
78A PRO* 4.2 22.3 - - + +
80A LYS 5.3 0.2 - - - +
127A ILE* 2.9 15.7 + - + +
128A GLY 3.6 7.0 - - - +
130A ALA* 1.3 74.1 - - - +
132A GLN* 1.3 62.4 + - - +
134A GLY* 3.0 18.4 + - - -
135A TYR 3.5 19.7 - - - +
137A VAL* 3.8 13.7 - - + -
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Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 5.3 0.2 + - - -
50A ASN* 2.6 45.1 + - - +
128A GLY 2.9 20.7 + - - +
129A TRP* 3.2 6.9 + - - +
131A LEU* 1.3 76.5 - - - +
133A GLN* 1.4 67.8 + - - +
134A GLY 3.1 1.4 + - - -
417A LEU* 4.4 12.8 - - + -
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Residues in contact with GLN 133 (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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82A ALA* 3.6 14.7 - - - +
129A TRP* 3.0 64.1 + - + +
130A ALA 3.5 4.3 - - - +
131A LEU 3.2 0.4 - - - -
132A GLN* 1.4 84.8 - - - +
134A GLY* 1.3 59.6 + - - +
135A TYR* 3.4 38.9 - - + +
382A LYS* 4.4 18.4 + - + +
412A VAL 4.8 2.1 + - - +
413A LEU 5.4 1.2 + - - -
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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