Contacts of the helix formed by residues 139 - 149 (chain B) in PDB entry 3ZRL
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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138B THR* 1.3 70.7 - - - +
140B TYR* 1.3 63.8 + - - +
142B VAL* 4.0 1.0 - - - +
143B ALA* 3.0 23.2 + - - +
161B TYR* 3.9 17.2 - - + -
184B PRO* 3.8 21.5 - - + +
187B LEU* 2.8 25.7 + - + +
189B LEU* 3.7 22.4 - - + +
196B LEU* 3.7 28.0 - - + -
246B VAL* 4.8 4.5 - - + -
250B LEU* 4.0 26.2 - - + -
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 3.1 6.3 - - - +
139B VAL* 1.3 80.6 - - - +
141B ARG* 1.3 80.5 + - - +
143B ALA* 3.8 4.1 - - + +
144B ARG* 3.1 62.7 + - + +
184B PRO* 3.3 18.5 + - + -
185B GLN* 3.4 55.4 - - + +
249B GLU* 4.8 8.1 - - - -
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Residues in contact with ARG 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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137B GLU* 4.5 20.4 - - + +
138B THR* 3.0 24.8 + - - +
140B TYR* 1.3 88.1 - - + +
142B VAL* 1.3 61.2 + - - +
144B ARG* 3.4 41.6 + - - +
145B HIS* 3.1 27.9 + - - +
1389B GOL 3.0 38.0 + - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 3.7 24.2 - - + +
138B THR 3.1 17.1 + - - +
139B VAL 4.0 2.2 - - - +
141B ARG* 1.3 73.7 - - - +
143B ALA* 1.3 65.5 + - - +
145B HIS* 3.3 7.3 + - - +
146B TYR* 3.2 36.4 + - + -
153B LEU* 3.9 20.0 - - + -
157B TYR* 6.3 0.2 - - + -
161B TYR* 3.8 22.9 - - + +
189B LEU* 3.8 15.5 - - + -
191B PRO* 5.8 6.5 - - + -
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Residues in contact with ALA 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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139B VAL* 3.0 19.3 + - + +
140B TYR* 3.8 5.8 - - + +
142B VAL* 1.3 78.3 - - - +
144B ARG* 1.3 56.6 + - - +
146B TYR* 3.3 8.0 + - - +
147B SER* 3.0 27.9 + - - -
153B LEU* 4.9 8.7 - - + -
184B PRO* 6.1 1.3 - - + -
249B GLU* 6.0 4.0 - - + +
250B LEU* 4.1 23.8 - - + -
253B GLY* 6.1 0.5 - - - -
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Residues in contact with ARG 144 (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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140B TYR* 3.1 49.9 + - + +
141B ARG* 3.4 45.5 + - - +
142B VAL 3.3 0.2 - - - -
143B ALA* 1.3 73.1 - - - +
145B HIS* 1.3 59.0 + - - +
147B SER* 3.6 7.5 - - - -
148B ARG* 2.8 86.2 + - + +
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Residues in contact with HIS 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 ARG 3.1 14.8 + - - +
142B VAL* 3.4 10.8 - - - +
144B ARG* 1.3 78.3 - - - +
146B TYR* 1.3 84.1 + + - +
148B ARG* 3.6 7.5 + - - +
149B ALA* 3.2 27.3 + - + +
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Residues in contact with TYR 146 (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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142B VAL* 3.2 30.9 + - + -
143B ALA 3.6 7.9 - - - +
144B ARG 3.3 0.2 - - - -
145B HIS* 1.3 93.3 - + - +
147B SER* 1.3 58.1 + - - +
149B ALA* 3.5 3.0 + - - -
150B LYS 3.3 4.0 + - - -
151B GLN* 2.7 77.3 + - + +
152B THR 4.1 2.5 - - - -
153B LEU* 3.5 30.3 - - + +
154B PRO* 3.5 33.7 - - + +
157B TYR* 4.4 12.8 - + - -
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Residues in contact with SER 147 (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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143B ALA 3.0 17.1 + - - -
144B ARG* 3.6 10.5 - - - -
146B TYR* 1.3 78.7 - - - +
148B ARG* 1.3 61.8 + - - +
150B LYS* 3.3 21.3 + - - +
151B GLN 3.8 7.2 + - - +
253B GLY* 3.6 27.2 + - - -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 2.8 73.2 + - + +
145B HIS* 4.0 7.2 - - - +
147B SER* 1.3 73.7 - - - +
149B ALA* 1.3 57.8 + - - +
150B LYS* 3.0 21.4 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS* 3.2 23.5 + - + +
146B TYR* 3.9 5.2 - - - +
147B SER 3.4 0.2 - - - -
148B ARG* 1.3 75.5 - - - +
150B LYS* 1.3 70.3 + - - +
151B GLN* 3.3 23.9 + - - +
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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