Contacts of the helix formed by residues 123 - 137 (chain T) in PDB entry 3P71
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 123 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C AN6 3.4 69.8 - + - -
23T ASP* 4.0 16.2 - - - -
26T VAL* 4.4 8.7 - - + -
27T ARG* 3.5 42.4 - - + +
122T ASP* 1.3 80.8 + - - +
124T PRO* 1.3 79.1 - - + +
125T MET* 4.3 1.3 - - + +
126T ILE* 2.9 14.8 + - + +
127T VAL* 3.0 10.6 + - - +
170T ALA 4.0 1.6 - - - -
171T ASP* 3.9 28.0 - - + -
173T ARG* 3.9 15.7 - - - -
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Residues in contact with PRO 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T ASP 3.6 2.9 - - - +
123T PHE* 1.3 92.8 - - + +
125T MET* 1.3 52.2 + - - +
127T VAL* 3.1 3.6 + - + +
128T THR* 2.8 41.1 + - - -
158T HIS* 3.7 34.8 + - + +
169T GLY* 4.1 23.3 - - - +
170T ALA* 4.2 9.2 - - - +
171T ASP* 5.1 0.9 - - + +
177T GLU* 5.5 3.4 - - - +
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Residues in contact with MET 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ARG* 3.6 35.2 - - + +
123T PHE* 4.9 0.2 - - + -
124T PRO* 1.3 80.3 - - - +
126T ILE* 1.3 63.6 + - + +
128T THR* 3.5 9.4 + - - -
129T ARG* 3.3 49.1 + - - +
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Residues in contact with ILE 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C AN6 3.9 9.6 - - - +
27T ARG* 3.8 39.7 - - + +
30T CYS* 4.1 17.5 - - + -
100T GLY* 4.3 7.0 - - - +
101T MET* 3.8 17.6 - - + +
122T ASP* 3.4 39.5 - - + +
123T PHE* 2.9 6.7 + - + +
125T MET* 1.3 73.5 - - + +
127T VAL* 1.3 67.0 + - - +
129T ARG* 3.0 35.7 + - - +
130T LYS* 3.1 12.0 + - + +
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Residues in contact with VAL 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T ASP* 3.6 14.4 - - + +
123T PHE 3.0 12.4 + - - +
124T PRO* 3.6 7.0 - - + +
126T ILE* 1.3 74.8 - - - +
128T THR* 1.3 51.3 + - - +
130T LYS* 2.9 8.2 + - - +
131T LEU* 2.7 57.1 + - + +
158T HIS* 3.6 22.9 - - - +
167T VAL* 3.8 23.6 - - + +
168T ILE 3.4 23.8 - - - +
169T GLY* 3.6 9.2 - - - +
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Residues in contact with THR 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T PRO 2.8 29.1 + - - -
125T MET* 3.6 11.4 - - - -
127T VAL* 1.3 72.3 - - - +
129T ARG* 1.3 62.7 + - - +
131T LEU* 4.0 7.6 - - - +
132T HIS* 3.2 23.8 + - + +
158T HIS* 3.4 23.3 + - + +
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Residues in contact with ARG 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ARG 5.9 0.2 + - - -
31T GLU* 5.1 11.7 + - - +
101T MET* 4.0 17.7 - - + +
125T MET* 3.3 37.1 + - - +
126T ILE* 3.0 25.9 + - - +
128T THR* 1.3 78.1 - - - +
130T LYS* 1.3 62.2 + - - +
132T HIS* 3.7 7.0 + - - +
133T SER* 3.4 23.0 + - - -
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Residues in contact with LYS 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T PHE* 3.5 32.5 - - + -
100T GLY 3.1 28.5 + - - +
101T MET* 4.2 11.4 - - + +
102T ASP 2.7 30.7 + - - +
106T TRP* 4.6 0.4 - - - -
120T GLU* 2.7 32.2 + - - +
126T ILE* 3.1 11.0 + - + +
127T VAL* 2.9 12.2 + - - +
129T ARG* 1.3 76.2 - - - +
131T LEU* 1.3 59.9 + - - +
133T SER* 3.6 2.1 + - - -
134T ILE* 3.1 35.4 + - + +
165T TYR* 3.9 9.6 - - - -
167T VAL* 4.7 11.7 - - + -
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Residues in contact with LEU 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T VAL* 2.7 38.2 + - + +
128T THR* 4.0 6.5 - - - +
130T LYS* 1.3 73.9 - - - +
132T HIS* 1.3 60.0 + - - +
134T ILE* 3.9 5.9 - - + +
135T LYS* 2.9 32.2 + - - +
155T MET* 3.4 39.2 - - + +
157T GLY 5.0 0.9 - - - +
158T HIS* 4.5 3.8 - - - -
159T ILE 4.2 8.7 - - - +
160T LEU* 3.6 44.0 - - + +
167T VAL* 4.1 17.0 - - + -
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Residues in contact with HIS 132 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128T THR 3.2 18.1 + - - +
129T ARG* 3.8 6.5 + - - +
131T LEU* 1.3 76.6 - - - +
133T SER* 1.3 65.3 + - - +
135T LYS* 3.8 3.2 - - - +
136T CYS* 2.9 67.9 + - + +
137T LYS* 5.7 5.2 - - - -
155T MET* 5.4 0.4 - - - -
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Residues in contact with SER 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53T HIS 3.1 25.9 + - - -
54T PHE* 3.7 27.9 + - - -
129T ARG 3.4 11.5 + - - -
130T LYS 3.8 2.7 - - - -
131T LEU 3.4 0.2 - - - -
132T HIS* 1.3 86.2 + - - +
134T ILE* 1.3 62.4 + - - +
136T CYS* 4.6 2.9 - - - -
137T LYS* 3.1 35.4 + - - +
140T LEU* 3.2 7.1 - - - +
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Residues in contact with ILE 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T PHE* 4.2 9.0 - - + -
106T TRP* 4.1 27.8 - - + -
130T LYS* 3.1 37.2 + - + +
131T LEU* 3.9 9.2 - - + +
132T HIS 3.3 0.2 - - - -
133T SER* 1.3 77.0 - - - +
135T LYS* 1.3 62.1 + - - +
137T LYS 3.2 18.7 - - - +
140T LEU* 3.8 7.0 - - + -
141T SER* 3.4 12.3 + - - -
144T ILE* 3.9 20.9 - - + -
153T LEU* 4.3 11.2 - - + -
155T MET* 5.3 0.4 - - - -
160T LEU* 4.0 28.0 - - + -
165T TYR* 4.3 12.1 - - + +
167T VAL* 4.5 2.0 - - + -
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Residues in contact with LYS 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T LEU 2.9 18.8 + - - +
132T HIS* 3.9 3.6 - - - +
134T ILE* 1.3 79.0 - - - +
136T CYS* 1.3 63.2 + - - +
138T PRO* 5.5 0.3 - - - +
141T SER* 4.8 6.8 + - - -
153T LEU* 4.4 26.2 + - + +
155T MET* 3.7 32.6 - - + +
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Residues in contact with CYS 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132T HIS* 2.9 54.6 + - + +
133T SER* 4.6 1.6 - - - -
135T LYS* 1.3 81.7 - - - +
137T LYS* 1.3 73.4 + - + +
138T PRO* 3.4 10.7 - - - +
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Residues in contact with LYS 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T GLN 4.8 2.6 + - - -
53T HIS* 3.2 53.9 + - + +
132T HIS* 5.7 5.2 - - - -
133T SER* 3.1 25.5 + - - +
134T ILE 3.2 7.2 - - - +
135T LYS 3.4 0.8 - - - -
136T CYS* 1.3 88.1 - - + +
138T PRO* 1.3 63.0 - - + +
139T PRO* 3.3 8.3 - - + -
140T LEU* 2.9 25.9 + - + +
141T SER* 3.2 10.0 + - - -
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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