Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 3EQR
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 THR 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ARG* 5.0 1.1 - - - +
144B GLU* 3.6 36.1 - - + +
145B TRP 3.3 9.6 - - - +
146B ASP* 3.5 25.5 + - - +
150B GLY 4.1 1.8 + - - -
151B LYS* 1.3 79.2 - - - +
153B VAL* 1.3 62.4 + - - +
154B SER 4.2 0.7 + - - -
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Residues in contact with VAL 153 (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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144B GLU* 3.4 4.9 - - - -
145B TRP* 2.8 51.0 + - + +
147B ALA* 3.9 16.6 - - + -
149B SER* 5.8 0.2 - - - +
151B LYS* 3.9 23.3 - - + +
152B THR* 1.3 77.9 - - - +
154B SER* 1.3 76.5 + - - +
155B VAL* 3.6 3.5 + - + +
193B TYR* 3.8 25.6 - - + +
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Residues in contact with SER 154 (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 ARG* 4.5 10.7 + - - -
143B GLY 3.8 8.3 + - - -
144B GLU* 4.9 2.9 - - - +
152B THR 4.2 1.0 + - - -
153B VAL* 1.3 80.0 - - - +
155B VAL* 1.3 63.0 + - - +
193B TYR* 4.4 2.4 + - - -
207B LEU* 3.3 37.8 + - - +
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Residues in contact with VAL 155 (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* 4.3 2.5 - - + -
142B ARG* 3.6 9.7 - - - +
143B GLY* 2.9 47.0 + - - +
144B GLU 3.9 9.6 - - - +
145B TRP* 3.8 17.9 - - + -
153B VAL* 3.8 10.5 - - + +
154B SER* 1.3 79.7 + - - +
156B ALA* 1.3 60.1 + - - +
157B VAL* 3.8 14.8 - - + -
193B TYR* 3.8 14.1 - - + -
204B VAL* 3.8 17.7 - - + -
205B THR 3.4 14.6 - - - +
207B LEU* 3.8 9.5 - - - +
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Residues in contact with ALA 156 (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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1B T74 3.3 49.2 - - + +
132B LEU* 4.2 2.0 - - + -
140B VAL* 4.1 7.0 - - + -
141B ARG 3.6 4.3 - - - -
155B VAL* 1.3 73.8 - - - +
157B VAL* 1.3 64.7 + - - +
204B VAL* 3.5 3.1 - - - -
205B THR* 2.9 37.8 + - - +
206B GLU 4.0 0.7 - - - +
207B LEU* 4.1 8.1 - - + +
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Residues in contact with VAL 157 (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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1B T74 4.0 2.0 - - - -
126B LEU* 4.2 11.7 - - + -
128B LEU* 3.8 24.9 - - + -
139B VAL 3.6 1.6 - - - +
140B VAL* 3.1 3.0 - - - +
141B ARG* 2.8 44.6 + - + +
143B GLY* 4.5 4.0 - - - -
155B VAL* 3.8 21.3 - - + -
156B ALA* 1.3 80.9 - - - +
158B LYS* 1.3 61.8 + - - +
159B CYS* 4.0 7.1 + - - -
202B LYS* 3.7 40.4 - - + -
203B MET 3.3 4.5 - - - +
204B VAL* 4.4 5.2 - - + -
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Residues in contact with LYS 158 (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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1B T74 3.2 35.5 + - + +
135B GLY* 3.8 16.1 - - - -
136B SER* 2.8 25.3 + - - +
137B PHE* 3.5 30.7 - - + -
138B GLY 3.9 5.6 - - - +
139B VAL 3.4 4.5 - - - +
140B VAL* 3.5 24.9 - - + +
157B VAL* 1.3 74.8 - - - +
159B CYS* 1.3 63.0 + - - +
177B GLU* 2.7 28.1 + - - -
202B LYS* 3.2 5.6 - - - -
203B MET* 2.9 34.7 + - + +
270B ASP* 4.7 6.3 + - - +
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Residues in contact with CYS 159 (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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128B LEU* 4.3 12.1 - - - -
137B PHE* 3.8 4.1 - - - -
138B GLY* 3.3 25.8 - - - -
139B VAL* 2.9 22.4 + - + +
141B ARG* 5.0 9.9 - - - -
157B VAL* 4.3 10.8 - - - -
158B LYS* 1.3 74.9 - - - +
160B LEU* 1.3 62.8 + - - +
161B LYS* 3.8 3.0 + - - +
200B PRO* 5.5 4.9 - - + -
201B MET 3.6 4.3 - - - +
202B LYS* 3.9 29.6 - - + +
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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