Contacts of the helix formed by residues 134 - 148 (chain X) in PDB entry 3F6E
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 GLU 134 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X TYR* 2.5 33.5 + - - -
129X PRO* 4.0 7.6 - - + -
130X ALA* 2.8 33.2 + - - +
131X SER* 3.2 20.3 + - - +
132X ALA 3.0 0.6 - - - -
133X ALA* 1.3 79.2 - - - +
135X VAL* 1.3 63.9 + - - +
136X PRO 3.4 0.4 - - - -
137X HIS* 3.1 22.0 + - + +
138X ALA* 2.9 21.9 + - + +
141X ARG* 4.3 7.4 + - - -
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Residues in contact with VAL 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 3.7 17.3 - - + -
8X THR* 4.0 5.2 - - + +
129X PRO* 3.9 20.9 - - + -
131X SER 4.0 2.5 - - - +
132X ALA 3.0 16.6 + - - +
134X GLU* 1.3 77.1 - - - +
136X PRO* 1.3 67.4 - - + +
138X ALA* 3.1 2.4 + - - +
139X MET* 2.9 21.7 + - + +
156X LEU* 4.7 4.2 - - + +
158X VAL* 3.9 19.1 - - + -
162X ASP* 3.4 28.7 - - + +
163X TRP* 3.9 24.5 - - + -
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Residues in contact with PRO 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 4.1 11.9 - - + -
7X THR* 3.7 34.8 - - + -
8X THR* 3.8 18.2 - - - +
11X LEU* 3.3 15.5 - - + +
132X ALA 4.0 3.8 - - - +
133X ALA 3.5 14.8 - - - +
135X VAL* 1.3 93.2 - - + +
137X HIS* 1.3 56.7 + - - +
139X MET* 3.2 5.0 + - + -
140X SER* 2.8 25.5 + - - -
167X ALA* 4.9 2.9 - - + -
171X SER* 4.0 7.9 - - - +
174X LEU* 3.6 14.1 - - + -
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Residues in contact with HIS 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X ALA 5.0 1.5 + - - +
134X GLU* 3.1 24.7 + - + +
136X PRO* 1.3 78.8 - - - +
138X ALA* 1.3 62.5 + - - +
140X SER* 3.2 3.4 + - - -
141X ARG* 3.0 47.3 + - + +
171X SER* 5.1 1.5 + - - +
174X LEU* 3.6 30.3 - - + +
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Residues in contact with ALA 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X TRP* 3.5 8.6 - - - -
127X TYR* 4.1 13.5 - - + -
129X PRO* 3.8 15.0 - - + -
134X GLU* 2.9 15.3 + - + +
135X VAL 3.5 7.4 - - - +
137X HIS* 1.3 77.1 + - - +
139X MET* 1.3 57.1 + - - +
141X ARG* 3.2 15.8 + - - +
142X ALA* 2.9 23.7 + - - +
156X LEU* 3.8 24.2 - - + +
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Residues in contact with MET 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X THR* 3.8 28.7 - - + -
11X LEU* 3.9 13.7 - - + -
12X LEU* 4.2 13.0 - - + -
31X PHE* 5.3 0.4 - - + -
66X PHE* 3.8 26.9 - - + -
93X ILE* 4.3 11.0 - - - -
95X THR* 3.7 24.0 - - + -
135X VAL* 2.9 14.5 + - + +
136X PRO* 3.2 10.5 + - + +
138X ALA* 1.3 77.4 - - - +
140X SER* 1.3 62.0 + - - +
142X ALA* 3.2 2.8 + - - +
143X ILE* 2.9 24.3 + - + +
156X LEU* 3.8 20.6 - - + +
158X VAL* 5.4 0.2 - - + -
163X TRP* 4.5 13.9 - - + -
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Residues in contact with SER 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LEU* 3.5 14.5 - - - +
136X PRO 2.8 13.5 + - - -
137X HIS* 3.2 11.5 + - - -
139X MET* 1.3 75.3 - - - +
141X ARG* 1.4 61.9 + - - +
143X ILE* 3.2 7.2 + - - +
144X HIS* 3.0 46.0 + - - -
174X LEU* 3.7 31.6 + - - +
177X ARG* 4.3 8.0 + - - -
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Residues in contact with ARG 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X TRP* 3.4 46.0 - - + +
127X TYR* 4.1 25.1 + - - -
134X GLU* 4.3 5.2 + - - -
137X HIS* 3.0 46.4 + - + +
138X ALA* 3.4 10.3 - - - +
140X SER* 1.4 76.0 - - - +
142X ALA* 1.3 57.6 + - - +
144X HIS* 3.4 3.9 + - - +
145X MET* 2.7 38.4 + - + +
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Residues in contact with ALA 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X ILE* 4.1 14.5 - - + +
125X TRP* 3.7 18.3 - - + -
138X ALA 2.9 13.3 + - - +
139X MET* 3.5 12.1 - - - +
141X ARG* 1.3 76.8 - - - +
143X ILE* 1.3 63.5 + - - +
145X MET* 4.7 0.9 - - - -
146X ALA* 2.9 21.0 + - - +
154X VAL* 3.5 26.8 - - + +
155X TYR 5.7 0.2 - - - +
156X LEU* 4.8 11.2 - - + -
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Residues in contact with ILE 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LEU* 3.9 28.3 - - + +
12X LEU* 4.1 17.5 - - + -
15X GLN* 4.0 41.1 - - + +
17X ILE* 4.0 9.6 - - + -
64X PRO* 5.2 3.1 - - + -
93X ILE* 3.8 24.2 - - + +
139X MET* 2.9 25.2 + - + +
140X SER* 3.6 7.2 - - - +
142X ALA* 1.3 78.0 - - - +
144X HIS* 1.3 67.9 + - + +
146X ALA* 3.3 2.4 + - - +
147X SER* 2.8 34.5 + - - +
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Residues in contact with HIS 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LEU* 6.0 0.2 - - - +
15X GLN* 3.4 29.3 + - - +
140X SER* 3.0 35.9 + - - +
141X ARG* 4.1 4.3 - - - +
143X ILE* 1.3 77.2 - - + +
145X MET* 1.3 68.5 + - - +
147X SER* 4.4 6.3 - - - -
148X MET* 2.9 40.7 + - + +
174X LEU 5.2 0.8 + - - -
177X ARG* 3.6 44.4 + - - +
179X VAL* 3.6 35.0 + - + +
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Residues in contact with MET 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LYS* 2.7 67.8 + - + +
125X TRP* 3.9 26.9 - - + -
141X ARG* 2.7 29.0 + - + +
142X ALA* 4.7 0.2 - - - -
144X HIS* 1.3 73.8 - - - +
146X ALA* 1.3 60.0 + - - +
147X SER 3.3 0.2 + - - -
148X MET* 3.7 20.4 - - + +
154X VAL* 3.8 17.3 - - + -
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Residues in contact with ALA 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X PRO* 5.0 0.4 - - + -
91X PRO* 3.4 9.3 - - + +
92X LEU 4.0 15.0 - - - +
93X ILE* 4.0 19.3 - - + -
142X ALA 2.9 17.8 + - - +
143X ILE 3.8 4.7 - - - +
144X HIS 3.2 0.2 - - - -
145X MET* 1.3 77.8 - - - +
147X SER* 1.3 59.1 + - - +
151X GLN* 3.4 11.4 - - - +
152X GLY 3.2 39.7 + - - +
154X VAL* 3.7 5.1 - - + +
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Residues in contact with SER 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X PRO* 3.3 28.4 - - - +
91X PRO* 4.6 1.3 - - - -
143X ILE* 2.8 25.0 + - - +
144X HIS* 3.1 8.6 + - - -
146X ALA* 1.3 77.1 - - - +
148X MET* 1.3 64.3 + - - +
149X ALA 3.8 0.7 + - - -
151X GLN* 2.9 28.2 + - - +
181X SER* 4.9 1.2 + - - -
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Residues in contact with MET 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124X LYS* 2.9 25.8 + - - +
144X HIS* 2.9 32.4 + - + +
145X MET* 3.7 30.3 + - + +
146X ALA 3.6 0.4 - - - -
147X SER* 1.3 77.5 - - - +
149X ALA* 1.3 65.7 + - - +
150X PRO 3.1 8.0 - - - -
151X GLN* 3.2 4.4 + - - -
179X VAL* 3.6 35.4 - - + +
180X SER 6.0 0.2 - - - +
181X SER* 3.9 14.8 - - - +
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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