Contacts of the helix formed by residues 139 - 152 (chain B) in PDB entry 4R0C
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 VAL 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B SER* 3.2 37.5 - - - +
107B ALA* 5.4 2.7 - - + -
135B ALA* 2.9 16.4 + - + +
138B VAL* 1.3 86.3 - - + +
140B LEU* 1.3 65.9 + - + +
142B PRO* 3.3 16.3 - - - +
143B LEU* 3.4 15.7 + - + +
52C ASP* 3.5 40.8 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.6 53.2 - - + +
107B ALA* 4.7 0.9 - - - +
110B VAL* 5.1 3.6 - - + -
122B VAL* 4.7 3.1 - - + +
125B ALA* 3.6 8.5 - - + -
126B GLY* 3.5 35.7 - - - +
129B SER* 4.4 4.0 - - - -
135B ALA* 2.7 15.8 + - + +
136B GLY* 3.4 14.8 - - - +
139B VAL* 1.3 78.5 - - + +
141B ILE* 1.3 65.2 + - - +
143B LEU* 4.0 15.0 - - + +
144B ALA* 3.4 22.5 + - - +
162B ALA* 4.1 6.1 - - + +
166B VAL* 4.4 2.5 - - + -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.6 9.9 - - - +
137B TYR* 3.1 31.2 + - + +
140B LEU* 1.3 76.7 - - - +
142B PRO* 1.4 67.6 - - + +
144B ALA* 3.6 2.9 + - - +
145B GLY 3.5 12.1 + - - -
159B ILE* 3.6 20.3 - - + +
162B ALA* 3.9 19.4 - - + +
163B PHE* 4.0 18.8 - - + +
166B VAL* 5.4 1.1 - - + -
445B VAL* 3.5 42.4 - - + -
448B PHE* 3.8 27.8 - - + -
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Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR 3.3 5.8 - - - +
138B VAL 3.1 28.5 - - - +
139B VAL* 3.3 9.2 - - - +
141B ILE* 1.4 89.4 - - + +
143B LEU* 1.3 64.3 + - - +
145B GLY* 2.9 15.3 + - - -
146B LEU* 3.0 13.4 + - - +
159B ILE* 5.2 2.5 - - + -
448B PHE* 3.4 31.0 - - + +
451B ARG* 6.5 1.3 - - - -
452B TYR* 4.4 4.4 + - + -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 3.7 39.7 - - + +
110B VAL* 4.1 18.8 - - + -
111B ARG* 3.6 8.5 - - - +
139B VAL* 3.4 18.8 + - + +
140B LEU* 4.0 12.6 - - + +
141B ILE 3.4 0.8 - - - -
142B PRO* 1.3 80.3 - - - +
144B ALA* 1.3 59.6 + - - +
146B LEU* 3.0 7.4 + - - +
147B VAL* 2.9 40.3 + - + +
49C PRO 3.3 24.7 - - - +
50C LEU* 3.4 19.1 - - + +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 5.2 1.3 - - + -
122B VAL* 3.6 28.3 - - + -
140B LEU 3.4 14.9 + - - +
141B ILE 3.9 2.9 - - - +
142B PRO 3.2 0.6 - - - -
143B LEU* 1.3 81.4 - - - +
145B GLY* 1.3 61.7 + - - +
147B VAL* 3.4 4.5 + - - +
148B PHE* 3.1 29.6 + - - +
158B GLY* 3.1 28.5 - - - +
162B ALA* 3.9 5.4 - - + -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE 3.5 4.8 + - - -
142B PRO 2.9 9.2 + - - -
144B ALA* 1.3 78.4 - - - +
146B LEU* 1.3 56.0 + - - +
148B PHE* 3.8 0.5 - - - +
149B GLN* 3.1 19.6 + - - +
155B PRO* 3.6 23.5 - - - +
158B GLY 4.3 0.2 - - - -
159B ILE* 4.1 7.2 - - - +
452B TYR* 3.2 31.1 + - - -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO 3.0 8.8 + - - +
143B LEU* 3.0 10.3 + - - +
145B GLY* 1.3 73.7 - - - +
147B VAL* 1.3 65.2 + - - +
148B PHE 3.0 2.0 + - - -
149B GLN* 3.2 5.3 + - + +
150B LEU* 3.1 46.3 + - + +
451B ARG* 4.2 12.3 - - - +
452B TYR* 3.1 18.1 + - + +
49C PRO* 4.4 27.1 - - + +
50C LEU* 3.4 30.5 - - + -
413C LEU* 3.9 20.0 - - + +
414C LEU* 5.9 1.3 - - + -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.2 23.8 - - + +
111B ARG* 4.7 6.5 - - - +
118B LEU* 3.9 30.7 - - + -
143B LEU* 2.9 40.0 + - + +
144B ALA* 4.1 3.6 - - - +
146B LEU* 1.3 76.3 - - - +
148B PHE* 1.3 58.8 + - + +
150B LEU* 3.7 8.0 + - - +
151B ALA* 3.2 24.8 + - + +
242B SER* 4.8 7.4 - - - -
50C LEU* 4.2 11.4 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.3 35.4 - - + -
119B VAL* 3.4 28.5 - - + -
122B VAL* 4.8 11.0 - - + -
144B ALA* 3.1 22.1 + - - +
145B GLY 3.8 4.7 - - - +
146B LEU 3.0 0.4 - - - -
147B VAL* 1.3 79.6 - - + +
149B GLN* 1.3 65.8 + - - +
151B ALA* 3.1 4.6 + - - +
152B GLY 3.1 3.3 + - - -
153B ARG* 2.9 42.4 + - + +
154B PRO 3.1 26.2 - - - +
155B PRO* 4.0 2.7 - - + -
157B ALA* 3.8 12.1 - - + -
158B GLY* 3.5 24.0 - - - -
161B THR* 4.9 1.8 - - + -
224B THR* 5.2 0.4 - - + -
229B GLU* 4.0 14.1 - - - -
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLY 3.1 16.3 + - - +
146B LEU* 3.2 13.4 + - + +
148B PHE* 1.3 74.8 - - - +
150B LEU* 1.3 64.4 + - + +
152B GLY* 2.9 22.3 + - - +
153B ARG 4.0 4.9 + - - +
155B PRO* 3.6 27.3 - - + +
452B TYR* 4.1 19.3 - - + +
375C LYS* 3.2 26.9 + - - -
414C LEU* 4.0 22.9 - - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 3.1 34.0 + - + +
147B VAL* 3.9 4.5 - - - +
149B GLN* 1.3 79.9 - - + +
151B ALA* 1.3 56.5 + - - +
152B GLY 3.3 0.2 - - - -
241B ALA* 2.9 13.7 + - - +
242B SER* 2.8 38.0 + - - +
243B VAL* 3.8 27.6 - - + +
50C LEU* 4.2 11.0 - - + -
375C LYS* 4.7 0.8 + - - -
412C MET 3.7 14.8 - - - +
413C LEU* 3.2 25.6 - - - +
414C LEU 4.0 1.8 - - - -
415C GLY* 3.4 26.0 - - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 5.1 7.2 - - + -
147B VAL 3.2 13.6 + - - +
148B PHE* 3.1 11.7 + - - +
150B LEU* 1.3 77.8 - - - +
152B GLY* 1.3 57.0 + - - +
153B ARG* 3.2 28.2 + - + +
237B THR* 5.6 0.7 + - - -
238B VAL 4.3 0.5 - - - +
240B ASP* 3.4 38.5 + - - +
242B SER* 4.6 2.9 - - - -
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE 3.7 0.2 - - - -
149B GLN* 2.9 17.5 + - - +
150B LEU 3.3 1.0 - - - -
151B ALA* 1.3 78.6 - - - +
153B ARG* 1.3 65.6 - - - +
154B PRO* 4.6 0.7 - - - +
237B THR* 5.4 7.3 + - - -
238B VAL* 4.0 23.8 + - - +
375C LYS* 4.1 8.0 - - - +
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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