Contacts of the helix formed by residues 131 - 144 (chain G) in PDB entry 6O81
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 SER 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ALA 3.3 6.9 + - - -
130G TYR* 1.3 83.3 - - - +
132G ARG* 1.3 65.6 + - - +
133G VAL* 3.3 9.4 + - - +
134G VAL* 3.3 26.2 + - - +
135G LEU* 3.4 15.8 + - - +
164G MET* 3.6 9.1 - - - +
196G GLY* 4.3 13.7 + - - -
197G ALA 6.0 0.4 - - - -
234G LYS* 5.8 3.8 - - - -
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Residues in contact with ARG 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASP* 3.4 29.8 - - - +
108G ARG* 3.4 28.1 + - - +
130G TYR* 4.9 8.6 - - + +
131G SER* 1.3 70.4 - - - +
133G VAL* 1.3 60.3 + - - +
135G LEU* 3.9 10.4 - - + +
136G ARG* 2.9 33.3 + - - +
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ARG* 3.4 13.2 - - + +
111G ILE* 3.7 28.7 - - + +
131G SER* 3.2 7.1 - - - +
132G ARG* 1.3 77.2 - - - +
134G VAL* 1.3 60.4 + - + +
136G ARG* 3.3 5.4 + - + +
137G VAL* 2.9 29.5 + - - +
196G GLY* 5.6 1.6 - - - -
229G VAL* 3.8 28.0 - - + +
231G GLU* 3.4 37.5 - - - +
234G LYS* 4.3 13.7 - - - +
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Residues in contact with VAL 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ILE* 6.1 0.4 - - + -
127G THR* 3.8 34.8 - - + +
128G HIS 6.2 0.2 - - - +
129G ALA 5.6 1.1 - - - +
131G SER* 3.3 21.7 + - - +
133G VAL* 1.3 71.9 - - - +
135G LEU* 1.3 61.3 + - - +
137G VAL* 3.3 8.3 - - + +
138G LEU* 2.9 39.8 + - + +
164G MET* 4.8 3.8 - - + -
194G ILE* 4.5 16.4 - - + +
195G VAL 4.5 0.7 - - - -
196G GLY* 3.6 29.4 - - - +
229G VAL* 3.8 10.1 - - + -
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASP* 5.2 11.2 - - - +
130G TYR* 3.7 28.7 - - + +
131G SER 3.4 13.8 + - - +
132G ARG* 4.0 7.2 - - + +
133G VAL 3.3 0.2 - - - -
134G VAL* 1.3 78.8 - - - +
136G ARG* 1.3 58.2 + - - +
138G LEU* 3.8 5.9 - - - +
139G GLU* 2.9 49.2 + - + +
164G MET* 4.2 18.0 - - + +
167G ALA* 4.0 23.3 - - + +
168G LEU* 4.6 15.0 - - + +
171G LEU* 5.2 4.3 - - + +
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Residues in contact with ARG 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASP* 5.1 14.6 + - - -
108G ARG* 3.4 44.7 - - + +
109G ASN* 3.2 25.8 + - - -
111G ILE* 6.1 0.9 - - + -
112G ALA* 3.7 21.8 - - + +
132G ARG* 2.9 22.7 + - - +
133G VAL* 3.6 6.5 - - - +
135G LEU* 1.3 79.9 - - - +
137G VAL* 1.3 57.3 + - - +
139G GLU* 3.3 29.6 + - - +
140G ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 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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111G ILE* 4.0 13.0 - - + +
112G ALA* 4.5 3.3 - - - +
115G CYS* 3.7 26.5 - - + -
116G HIS* 3.7 31.0 - - + +
119G ILE* 4.8 5.6 - - + +
133G VAL 2.9 17.2 + - - +
134G VAL* 3.3 24.5 - - + +
136G ARG* 1.3 75.9 - - - +
138G LEU* 1.3 62.9 + - + +
140G ALA* 3.5 4.9 + - - +
141G ALA* 2.9 27.1 + - - +
194G ILE* 5.0 10.5 - - + -
229G VAL* 5.0 3.4 - - + -
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Residues in contact with LEU 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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119G ILE* 5.3 6.7 - - + -
125G ILE* 4.7 17.5 - - + -
127G THR* 4.4 5.8 - - + +
134G VAL* 2.9 36.1 + - + +
135G LEU* 3.9 4.7 - - - +
137G VAL* 1.3 81.1 - - + +
139G GLU* 1.3 60.0 + - - +
141G ALA* 3.2 4.1 + - + +
142G VAL* 2.9 34.7 + - + +
148G PHE* 3.6 28.4 - - + -
150G VAL* 4.3 17.5 - - + -
164G MET* 5.8 1.3 - - - -
168G LEU* 3.8 35.4 - - + -
171G LEU* 5.2 1.1 - - - -
194G ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 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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135G LEU* 2.9 32.9 + - - +
136G ARG* 3.3 41.1 + - - +
138G LEU* 1.3 75.7 - - - +
140G ALA* 1.3 58.4 + - + +
142G VAL* 3.4 12.1 - - + +
143G ALA* 2.9 28.2 + - - +
171G LEU* 3.7 21.7 - - + +
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Residues in contact with ALA 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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112G ALA* 3.5 36.6 - - + +
116G HIS* 3.6 16.0 - - + -
136G ARG 2.9 19.1 + - - +
137G VAL 3.7 4.5 - - - +
139G GLU* 1.3 78.7 - - + +
141G ALA* 1.3 62.7 + - - +
143G ALA* 3.4 8.0 + - - +
144G ALA* 3.4 14.7 + - - +
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Residues in contact with ALA 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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116G HIS* 4.0 15.7 - - + +
119G ILE* 4.4 14.8 - - + -
137G VAL 2.9 18.0 + - - +
138G LEU* 3.2 7.4 + - + +
140G ALA* 1.3 77.7 - - - +
142G VAL* 1.3 60.4 + - - +
144G ALA* 3.3 10.4 + - - -
146G LYS* 3.4 30.9 + - + +
148G PHE* 3.7 22.7 - - + -
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G LEU* 2.9 15.6 + - + +
139G GLU* 3.4 15.3 - - + +
141G ALA* 1.3 72.4 - - - +
143G ALA* 1.3 66.0 + - - +
144G ALA 3.2 0.2 - - - -
145G LYS* 3.6 9.8 + - - -
146G LYS 4.2 14.4 - - - +
148G PHE* 3.6 22.7 - - + -
171G LEU* 3.7 33.2 - - + +
173G VAL* 4.9 7.0 - - + -
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Residues in contact with ALA 143 (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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139G GLU 2.9 19.7 + - - +
140G ALA* 3.6 10.8 - - - +
141G ALA 3.2 0.6 - - - -
142G VAL* 1.3 78.3 - - - +
144G ALA* 1.3 56.5 + - - +
145G LYS* 3.3 3.3 + - - +
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Residues in contact with ALA 144 (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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116G HIS* 4.1 19.7 - - + +
140G ALA 3.4 9.2 + - - +
141G ALA 3.3 10.1 + - - +
142G VAL 3.2 0.8 - - - -
143G ALA* 1.3 76.3 - - - +
145G LYS* 1.3 70.2 + - - +
146G LYS* 3.6 14.9 - - - +
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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