Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 4QKB
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 SER 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B PRO* 1.3 77.9 - - - +
142B VAL* 1.3 63.3 + - - +
143B MSE 4.2 0.2 - - - -
158B LEU* 3.8 4.8 - - - +
159B LEU* 2.8 40.8 + - - +
179B ILE* 3.6 23.0 - - - +
185B SER* 5.0 0.2 - - - -
192B ILE* 4.3 5.2 - - - -
194B ARG* 3.6 24.2 - - - +
197B ARG* 3.4 26.6 + - - -
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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
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141B SER* 1.3 80.3 - - - +
143B MSE 1.3 68.4 + - - +
144B ARG 3.7 1.0 + - - -
156B GLU* 4.1 17.3 - - + +
157B LEU 3.4 11.2 - - - +
158B LEU* 4.6 2.2 - - + -
178B GLU 3.7 0.2 - - - +
179B ILE* 3.5 6.1 - - - -
180B LEU* 3.2 45.2 + - + +
185B SER* 4.4 4.2 + - - +
186B PHE 3.6 36.6 - - - +
187B PHE* 3.9 9.0 - - + +
192B ILE* 3.9 23.8 - - + -
194B ARG* 5.2 0.4 - - - +
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Residues in contact with MSE 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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141B SER 4.2 0.6 - - - -
142B VAL* 1.3 71.9 - - - +
144B ARG* 1.3 61.6 + - - +
145B LEU* 4.0 5.2 + - + -
156B GLU* 3.4 1.0 - - - -
157B LEU* 2.7 54.1 + - + +
159B LEU* 3.8 11.1 - - + +
165B TYR* 3.4 51.4 - - + +
167B LEU* 4.1 9.2 - - - -
177B HIS* 3.9 29.8 - - + -
178B GLU 3.0 13.7 - - - +
179B ILE* 3.6 26.7 - - + +
302B AKG 3.6 14.4 - - + +
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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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142B VAL 3.7 3.0 + - - -
143B MSE 1.3 72.8 - - - +
145B LEU* 1.3 60.5 + - - +
146B VAL* 3.8 20.5 + - + +
154B TRP* 4.9 9.0 - - + -
155B LEU 3.3 14.8 - - - +
156B GLU* 4.2 27.1 + - + +
176B SER* 3.7 0.7 + - - +
177B HIS* 3.4 2.6 - - - -
178B GLU* 3.0 66.9 + - + +
180B LEU* 3.8 32.7 - - + +
184B GLU* 4.3 11.9 + - - +
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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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29B LEU* 5.5 1.3 - - + -
33B ALA* 4.1 14.4 - - + -
143B MSE 4.0 4.0 + - + -
144B ARG* 1.3 73.7 - - - +
146B VAL* 1.3 61.9 + - - +
154B TRP* 3.2 6.4 - - - +
155B LEU* 2.7 53.3 + - + +
157B LEU* 3.7 33.2 - - + -
167B LEU* 3.9 18.4 - - + -
171B ALA* 3.9 22.7 - - + +
175B PHE* 4.3 13.6 - - + -
176B SER 3.0 20.0 - - - +
177B HIS* 3.5 20.6 - - + -
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Residues in contact with VAL 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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120B PRO* 6.3 0.9 - - + -
144B ARG* 3.8 27.4 - - + +
145B LEU* 1.3 79.5 - - - +
147B HIS* 1.3 75.5 + - - +
148B THR 3.4 0.2 + - - -
151B PRO* 3.7 28.9 - - + +
153B GLU 3.8 4.0 - - - +
154B TRP* 4.0 7.4 - - + -
175B PHE* 3.4 4.7 - - - -
176B SER* 2.8 48.4 + - - +
178B GLU* 4.4 7.6 - - - +
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Residues in contact with HIS 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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28B ARG* 4.0 23.6 - - - -
146B VAL* 1.3 82.8 - - - +
148B THR* 1.3 65.7 + - - +
149B GLN* 3.0 38.6 + - + +
150B GLU* 3.3 38.1 + - + +
151B PRO* 4.0 2.6 - - - +
153B GLU* 3.0 25.1 + - + +
174B ASP* 3.7 21.7 + - + +
175B PHE* 3.2 30.4 - - + -
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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