Contacts of the strand formed by residues 139 - 149 (chain B) in PDB entry 4ZDH
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 LYS 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A MET* 3.8 22.2 - - + -
167A MET* 4.0 21.0 - - + -
169A PHE* 3.8 48.3 - - + -
133B GLU* 3.5 8.6 - - - +
134B ILE* 3.5 21.3 - - - -
137B THR* 3.0 30.7 + - - +
138B GLN* 1.3 83.7 - - + +
140B ALA* 1.3 61.5 + - - +
194B ARG* 3.6 19.3 - - + +
195B VAL 3.5 8.5 - - - +
196B SER* 5.0 0.7 - - - -
197B ALA 3.9 2.0 - - - +
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Residues in contact with ALA 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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129B PRO* 3.8 19.1 - - + -
133B GLU* 3.7 2.0 - - - -
134B ILE* 4.1 8.3 - - + -
139B LYS* 1.3 76.2 - - - +
141B THR* 1.3 63.0 + - - +
142B LEU* 3.8 1.1 + - - +
193B LEU 3.8 1.0 - - - +
194B ARG* 3.3 3.1 - - - -
195B VAL* 2.7 44.3 + - + +
196B SER 4.3 2.7 - - - +
197B ALA* 4.5 1.3 - - - -
200B TRP* 3.6 31.0 - - + -
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Residues in contact with THR 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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124A LEU* 3.3 19.8 - - - +
136A LEU* 3.6 25.8 - - + +
138A THR* 5.2 1.4 + - - +
162A LEU* 5.1 2.2 - - + -
129B PRO* 3.4 15.0 - - - +
133B GLU* 2.7 34.6 + - - +
140B ALA* 1.3 72.3 - - - +
142B LEU* 1.3 71.5 + - - +
143B VAL* 4.4 2.9 - - + -
192B ARG* 4.0 20.0 - - + -
193B LEU 3.6 4.9 - - - +
194B ARG* 3.1 23.9 + - + +
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Residues in contact with LEU 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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126B LEU* 3.6 23.8 - - + -
127B PHE 3.5 6.7 - - - +
129B PRO* 3.7 20.6 - - + -
140B ALA 4.3 5.8 - - - +
141B THR* 1.3 74.4 - - - +
143B VAL* 1.3 63.2 + - - +
158B TRP* 3.9 15.4 - - + -
192B ARG* 3.3 5.0 - - - -
193B LEU* 2.8 47.5 + - + +
195B VAL* 4.4 7.4 - - + -
200B TRP* 3.9 18.6 - - + -
207B PHE* 3.8 45.3 - - + -
238B ALA* 4.4 1.8 - - + -
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Residues in contact with VAL 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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124A LEU* 3.9 21.5 - - + -
134A VAL* 4.3 20.2 - - + -
136A LEU* 4.3 10.8 - - + -
175A VAL* 4.2 35.0 - - + -
126B LEU* 3.4 2.4 - - - +
127B PHE* 2.7 43.0 + - + -
141B THR* 4.1 2.7 + - + -
142B LEU* 1.3 78.0 - - - +
144B CYS* 1.3 70.9 + - - +
145B LEU* 4.6 2.9 - - + +
158B TRP* 4.2 3.4 - - - -
190B SER* 4.7 1.6 - - - -
191B SER 3.4 7.9 - - - +
192B ARG* 4.2 10.5 - - + -
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Residues in contact with CYS 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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124B VAL* 3.9 17.0 - - - -
125B ALA 3.5 5.2 - - - -
126B LEU* 4.5 0.4 - - - +
143B VAL* 1.3 75.2 - - - +
145B LEU* 1.3 65.1 + - - +
146B ALA 4.2 0.2 - - - -
156B LEU* 4.0 8.6 - - - +
158B TRP* 3.5 18.7 - - + -
189B LEU 4.0 0.3 - - - +
190B SER* 3.2 7.4 - - - -
191B SER* 2.9 37.1 + - - +
209B CYS* 2.0 51.1 - - + -
211B VAL* 4.7 0.7 - - - -
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Residues in contact with LEU 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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132A LYS* 4.8 5.4 - - - -
134A VAL* 3.9 22.2 - - + -
175A VAL* 5.2 1.8 - - + -
177A TRP* 3.8 53.6 - - + -
123B GLU 3.6 0.7 - - - +
124B VAL* 3.3 3.5 - - - -
125B ALA* 2.8 34.5 + - + +
127B PHE* 3.8 22.2 - - + -
143B VAL* 4.1 2.0 + - + -
144B CYS* 1.3 77.1 - - - +
146B ALA* 1.3 60.5 + - - +
147B THR* 3.7 20.1 + - + +
189B LEU 3.6 15.3 - - - +
190B SER* 4.0 10.8 - - - -
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Residues in contact with ALA 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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122B PRO* 4.1 10.8 - - + -
123B GLU 3.1 8.7 - - - +
124B VAL* 4.0 14.1 - - + -
144B CYS* 4.2 0.6 - - - -
145B LEU* 1.3 74.8 - - - +
147B THR* 1.3 61.9 + - - +
149B PHE* 3.6 11.5 - - + -
156B LEU* 5.2 3.1 - - + +
188B ALA* 3.2 2.8 - - - -
189B LEU* 2.8 47.8 + - + +
211B VAL* 4.2 17.3 - - + -
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Residues in contact with THR 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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177A TRP* 4.3 11.2 - - + +
122B PRO* 3.3 3.5 - - - +
123B GLU* 2.9 44.3 + - - +
145B LEU* 3.7 28.5 - - + -
146B ALA* 1.3 80.8 - - - +
148B GLY* 1.3 64.5 + - - +
149B PHE* 3.3 4.0 - - - -
178B GLU* 3.5 9.0 - - - +
187B TYR 3.6 4.5 - - - -
188B ALA* 4.1 11.2 - - + +
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Residues in contact with GLY 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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120B PHE* 3.3 8.3 - - - +
121B PRO 3.8 3.5 - - - +
123B GLU* 6.2 0.4 - - - -
147B THR* 1.3 72.5 - - - +
149B PHE* 1.3 59.5 + - - +
178B GLU* 2.8 28.0 + - - -
186B ARG* 2.7 44.1 + - - -
187B TYR 2.9 3.5 + - - -
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Residues in contact with PHE 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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120B PHE 3.3 11.7 - - - +
121B PRO 4.1 0.9 - - - -
122B PRO* 3.5 36.3 - - + -
146B ALA* 3.6 21.8 - - + -
147B THR 3.3 4.2 - - - -
148B GLY* 1.3 78.6 - - - +
150B TYR* 1.3 63.6 + - - +
151B PRO 3.5 14.6 - - - -
152B ASP* 3.8 11.9 - - + -
154B VAL* 3.6 36.8 - - + -
175B PRO* 4.2 3.6 - - + -
186B ARG* 3.4 1.5 - - - -
187B TYR* 2.7 64.0 + - + -
188B ALA* 3.7 5.2 - - - -
189B LEU* 3.8 15.7 - - + -
213B PHE* 4.3 2.5 - - + -
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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