Contacts of the helix formed by residues 122 - 134 (chain B) in PDB entry 3RC0
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 TRP 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B SER* 3.0 32.1 + - - +
121B GLY* 1.3 78.5 - - - +
123B VAL* 1.3 60.0 + - - +
124B PRO* 3.4 2.2 - - - -
125B LEU* 3.2 9.9 + - + +
126B LEU* 2.9 42.8 + - + +
217B VAL* 4.0 15.0 - - + -
220B VAL* 3.7 27.1 - - + -
221B MET* 3.5 41.1 - - + -
224B SER* 5.4 2.0 - - - -
241B PRO* 3.5 33.5 - - + +
296B MET* 4.2 11.4 - - + -
478B EDO 3.9 16.4 - - - -
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Residues in contact with VAL 123 (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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116B LEU* 3.5 26.7 - - + +
118B SER* 3.7 21.8 - - - +
121B GLY 3.5 0.4 - - - -
122B TRP* 1.3 76.3 - - - +
124B PRO* 1.3 67.5 - - + +
126B LEU* 3.2 7.4 + - + +
127B LEU* 2.8 48.7 + - + +
187B GLU* 3.9 24.5 - - + +
191B ILE* 4.3 9.9 - - + -
192B VAL* 4.1 15.5 - - + -
213B TYR* 4.2 6.7 - - - +
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Residues in contact with PRO 124 (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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100B GLN* 3.7 37.2 - - + +
109B LEU* 3.5 16.8 - - + +
113B ARG* 5.8 3.1 - - + +
116B LEU* 4.0 30.7 - - + +
121B GLY* 4.0 10.1 - - - +
122B TRP 3.7 2.0 - - - -
123B VAL* 1.3 97.4 - - + +
125B LEU* 1.3 56.3 + - - +
127B LEU* 3.3 3.4 + - + +
128B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU 4.0 20.4 - - - +
99B SER* 4.2 13.2 - - - -
100B GLN* 4.1 11.5 + - - +
122B TRP* 3.2 11.6 + - - +
124B PRO* 1.3 77.6 - - - +
126B LEU* 1.3 59.7 + - + +
128B ALA* 3.2 5.1 + - + +
129B LEU* 2.9 41.6 + - + +
220B VAL* 3.8 27.6 - - + -
241B PRO* 3.5 49.4 - - + +
243B MET* 4.3 12.1 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 2.9 39.6 + - + +
123B VAL* 3.7 5.4 - - - +
125B LEU* 1.3 77.4 - - - +
127B LEU* 1.3 56.7 + - + +
129B LEU* 3.3 6.2 + - + +
130B LEU* 2.8 36.8 + - + +
187B GLU* 4.7 0.2 - - - +
192B VAL* 5.8 0.7 - - + -
213B TYR* 3.5 36.1 - - + +
216B LEU* 3.7 31.0 - - + +
217B VAL* 3.9 18.4 - - + +
220B VAL* 3.7 26.2 - - + -
478B EDO 4.2 4.0 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.7 2.2 - - - -
109B LEU* 4.0 15.5 - - + -
116B LEU* 3.7 31.0 - - + -
123B VAL* 2.8 28.4 + - + +
124B PRO 3.8 3.1 - - - +
126B LEU* 1.3 72.6 - - - +
128B ALA* 1.3 60.2 + - - +
130B LEU* 4.3 5.6 - - + -
131B HIS* 2.9 31.4 + - - +
192B VAL* 4.1 27.4 - - + +
195B PHE* 3.8 23.8 - - + -
196B MET* 4.2 7.4 - - + -
203B PHE* 3.5 28.2 - - + -
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Residues in contact with ALA 128 (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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98B LEU* 5.0 2.7 - - + -
99B SER 4.0 4.0 - - - +
100B GLN* 4.0 13.5 - - - +
103B CYS* 3.6 35.2 - - + +
105B ILE* 4.8 0.4 - - - -
109B LEU* 4.0 3.4 - - + +
124B PRO 2.9 14.6 + - - +
125B LEU* 3.3 11.7 - - + +
127B LEU* 1.3 76.4 - - - +
129B LEU* 1.3 56.8 + - + +
131B HIS* 3.4 4.0 + - - +
132B GLU* 3.0 35.7 + - - +
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Residues in contact with LEU 129 (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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98B LEU* 3.6 30.1 - - + -
125B LEU* 2.9 24.3 + - + +
126B LEU* 3.3 13.0 + - + +
128B ALA* 1.3 72.9 - - - +
130B LEU* 1.3 66.7 + - - +
132B GLU* 3.1 5.3 + - - +
133B LEU* 2.9 39.3 + - + +
144B PHE* 4.9 0.2 - - + -
147B TRP* 4.0 11.9 - - + -
216B LEU* 4.7 9.0 - - + -
219B LEU* 4.5 16.8 - - + -
220B VAL* 3.7 30.1 - - + -
243B MET* 3.9 19.3 - - + -
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Residues in contact with LEU 130 (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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126B LEU* 2.8 29.8 + - + +
127B LEU* 3.8 8.1 - - + +
129B LEU* 1.3 73.3 - - - +
131B HIS* 1.3 62.1 + - - +
133B LEU* 3.6 8.0 + - + +
134B GLN* 3.3 18.5 + - - +
192B VAL* 4.2 25.1 - - + -
196B MET* 4.3 9.9 - - + -
203B PHE* 4.1 14.6 - - + -
207B VAL* 3.7 32.5 - - + +
212B LEU* 3.9 13.2 - - + -
213B TYR* 4.2 18.6 - - + +
216B LEU* 3.3 25.8 - - + -
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Residues in contact with HIS 131 (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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104B SER* 2.7 30.4 + - - -
105B ILE* 3.6 41.6 - - + +
127B LEU 2.9 18.4 + - - +
128B ALA 3.7 3.4 - - - +
130B LEU* 1.3 78.1 - - - +
132B GLU* 1.3 74.9 + - + +
133B LEU 3.2 0.7 + - - -
134B GLN* 2.7 38.5 + - - +
135B ALA* 3.2 12.7 + - + +
202B LEU* 2.9 38.8 + - + +
203B PHE* 3.7 10.2 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.8 21.5 - - + -
103B CYS* 3.4 3.9 - - + +
104B SER* 2.7 45.4 + - - -
128B ALA 3.0 21.6 + - - +
129B LEU 3.1 2.2 + - - +
131B HIS* 1.3 79.2 - - - +
133B LEU* 1.3 58.4 + - - +
134B GLN 3.4 0.5 + - - -
135B ALA* 3.5 4.5 + - - +
138B SER* 2.7 41.0 + - - +
139B ARG 4.2 0.5 + - - -
140B TRP* 3.6 16.6 - - + -
141B ARG* 3.0 21.8 + - - -
144B PHE* 3.6 21.8 - - + -
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Residues in contact with LEU 133 (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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397A GLU* 3.6 7.6 - - - +
129B LEU* 2.9 21.9 + - + +
130B LEU* 4.0 6.1 - - + +
131B HIS 3.2 0.4 - - - -
132B GLU* 1.3 79.3 - - - +
134B GLN* 1.3 56.9 + - - +
135B ALA 3.5 0.2 - - - -
141B ARG* 3.2 20.7 + - - +
144B PHE* 3.9 25.1 - - + -
147B TRP* 3.7 26.7 - - + -
150B LEU* 5.7 2.2 - - + -
207B VAL* 4.8 6.9 - - + +
212B LEU* 5.5 6.7 - - + -
216B LEU* 3.9 37.9 - - + -
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Residues in contact with GLN 134 (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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397A GLU* 3.2 15.3 - - - +
398A GLY* 3.0 26.7 + - - -
399A SER 4.4 6.1 + - - -
130B LEU 3.3 16.6 - - - +
131B HIS* 2.7 27.7 + - - -
133B LEU* 1.3 77.4 - - - +
135B ALA* 1.3 63.8 + - - +
201B ASP 4.6 2.3 + - - +
202B LEU* 3.2 23.5 + - - +
203B PHE* 3.4 1.9 + - - -
204B SER* 2.8 47.6 + - - +
207B VAL* 3.6 18.4 - - + -
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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