Contacts of the helix formed by residues 133 - 141 (chain G) in PDB entry 1GUM
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 PHE 133 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102G LEU* 4.5 12.3 - - + -
128G ALA* 2.8 25.6 + - + +
129G ILE* 4.5 0.7 - - + -
132G TYR* 1.3 73.7 - - + +
134G PRO* 1.3 72.4 - - + +
136G PHE* 3.3 5.8 + + - -
137G GLU* 2.8 22.9 + - - +
160G LEU* 4.6 7.0 - - + -
163G THR* 5.9 0.2 - - + -
164G ILE* 3.9 33.7 - - + -
167G LEU* 3.9 19.1 - - + -
174G ILE* 3.7 30.3 - - + -
175G LEU* 3.7 22.0 - - + -
178G PHE* 3.6 25.8 - + + -
181G LEU* 3.2 22.5 - - + +
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Residues in contact with PRO 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ALA 3.4 2.9 - - - +
129G ILE 3.0 26.9 - - - +
130G ILE 3.5 15.3 - - - +
131G ARG 4.7 1.6 - - - +
132G TYR 3.1 7.0 - - - +
133G PHE* 1.3 100.7 - - + +
135G VAL* 1.3 61.7 + - + +
137G GLU* 3.9 3.6 - - + +
138G LYS* 3.0 25.6 + - - +
178G PHE* 4.0 12.8 - - + -
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Residues in contact with VAL 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TYR* 5.3 0.7 - - + -
131G ARG 3.4 24.5 - - - +
132G TYR 2.8 10.8 + - - +
134G PRO* 1.3 74.2 - - + +
136G PHE* 1.3 68.2 + - + +
138G LYS* 3.5 5.6 + - - +
139G ILE* 3.1 40.4 + - + +
51H LEU* 3.6 45.5 - - + +
52H PHE* 3.8 18.6 - - + -
53H GLN* 5.6 1.8 - - - +
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Residues in contact with PHE 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TYR* 4.0 32.3 - + + -
99G THR* 3.7 19.7 - - + -
132G TYR* 3.3 36.5 + + + -
133G PHE* 3.9 7.4 - + - +
134G PRO 3.2 0.4 - - - -
135G VAL* 1.3 77.6 - - + +
137G GLU* 1.3 66.0 + - - +
139G ILE* 3.0 18.2 + - + +
140G LEU* 2.9 27.8 + - - +
148G LEU* 4.1 20.0 - - + -
160G LEU* 3.8 32.1 - - + -
181G LEU* 4.0 18.4 - - + -
52H PHE* 4.0 22.7 - + - -
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Residues in contact with GLU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G PHE 2.8 20.9 + - - +
134G PRO* 3.9 4.3 - - + +
136G PHE* 1.3 70.6 - - - +
138G LYS* 1.3 59.8 + - - +
140G LEU* 3.1 2.2 + - - +
141G ARG* 2.7 35.7 + - + +
177G ALA 4.2 0.9 - - - +
178G PHE* 2.8 32.8 - - + +
179G PRO* 2.9 20.1 - - - +
180G PHE* 2.8 42.8 + - + +
181G LEU* 2.7 30.3 + - - +
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Residues in contact with LYS 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G PRO 3.0 16.9 + - - +
135G VAL* 3.6 5.6 - - - +
137G GLU* 1.3 77.2 - - - +
139G ILE* 1.3 53.6 + - + +
141G ARG* 3.0 7.2 + - - +
142G GLY* 2.7 34.5 + - - -
48H ASN* 4.7 14.1 - - - +
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Residues in contact with ILE 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TYR* 3.4 34.5 - - + +
135G VAL* 3.1 36.4 + - + +
136G PHE* 3.0 19.2 + - + +
138G LYS* 1.3 78.2 - - + +
140G LEU* 1.3 65.1 + - - +
142G GLY* 3.2 8.4 + - - -
143G HIS* 3.3 27.1 + - + +
148G LEU* 3.7 37.0 - - + +
51H LEU* 5.7 0.7 - - + -
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G PHE 2.9 11.6 + - - +
137G GLU 3.5 6.1 - - - +
139G ILE* 1.3 76.4 - - - +
141G ARG* 1.3 61.3 + - - +
143G HIS* 3.8 11.6 + - + -
144G GLY* 2.9 33.3 + - - -
145G GLN 3.9 19.0 - - - +
147G PHE 4.0 3.8 - - - +
148G LEU* 3.8 22.0 - - + -
180G PHE* 4.2 24.7 - - + +
181G LEU* 4.0 19.5 - - + -
184G TYR* 3.6 47.1 - - + -
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Residues in contact with ARG 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ASP* 3.8 31.1 + - - -
137G GLU* 2.7 22.6 + - - +
138G LYS* 3.5 7.6 - - - +
140G LEU* 1.3 77.9 - - - +
142G GLY* 1.3 63.3 + - - +
143G HIS 3.5 0.7 + - - -
144G GLY* 4.2 3.6 + - - -
180G PHE* 3.3 46.2 - - + -
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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