Contacts of the strand formed by residues 154 - 159 (chain A) 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 TRP 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.7 26.7 - - + -
20A GLY 3.8 16.2 - - - -
21A SER* 3.0 46.9 + - - -
25A VAL* 3.6 10.4 - - - +
144A ARG* 4.6 8.1 - - + -
145A LEU 3.0 13.7 - - - +
146A VAL* 4.0 17.0 - - + -
151A PRO 3.7 13.5 - - - -
152A GLY* 3.5 13.9 + - - -
153A GLU* 1.3 73.1 - - - +
155A LEU* 1.3 74.4 + - - +
156A GLU* 4.0 24.0 - - + -
175A PHE* 4.6 1.8 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.3 6.3 - - + -
19A ARG 3.2 8.1 - - - +
20A GLY* 3.6 22.2 - - - -
25A VAL* 4.0 22.7 - - + +
26A LEU* 3.7 20.4 - - + -
29A LEU* 3.6 31.0 - - + +
33A ALA* 3.9 20.6 - - + +
144A ARG* 3.3 7.3 - - - +
145A LEU* 2.8 45.2 + - + -
154A TRP* 1.3 79.8 - - - +
156A GLU* 1.3 58.9 + - - +
157A LEU* 4.3 11.7 - - + -
175A PHE* 5.6 0.2 - - + -
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.4 4.0 - - - +
19A ARG* 2.7 42.0 + - + +
142A VAL* 4.1 12.1 - - + -
143A MSE 3.5 3.6 - - - -
144A ARG* 3.7 37.8 + - + -
154A TRP* 4.0 16.0 - - + -
155A LEU* 1.3 73.2 - - - +
157A LEU* 1.3 64.4 + - - +
180A LEU* 4.9 1.1 - - + +
186A PHE* 3.7 17.8 - - - +
187A PHE* 3.8 10.5 - - + -
188A GLY* 2.9 32.4 + - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TRP 3.3 3.6 - - - -
18A VAL* 3.9 22.0 - - + -
33A ALA* 4.5 10.5 - - + +
34A VAL 5.0 1.6 - - - +
35A VAL* 3.8 30.3 - - + -
142A VAL* 3.6 4.7 - - - +
143A MSE 2.7 54.3 + - + +
145A LEU* 4.0 20.0 - - + -
155A LEU* 4.4 7.6 - - + -
156A GLU* 1.3 81.5 - - - +
158A LEU* 1.3 62.1 + - - +
159A LEU* 3.7 6.2 + - + +
165A TYR* 4.7 6.3 - - + -
167A LEU* 4.0 26.9 - - + -
187A PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MSE 4.1 15.3 - - - +
17A TRP* 2.7 23.0 + - + +
35A VAL* 3.9 13.0 - - - +
37A PRO* 6.0 0.5 - - - +
140A PRO* 4.9 3.1 - - + -
141A SER 4.0 10.8 - - - +
142A VAL* 4.9 0.4 - - - -
157A LEU* 1.3 71.8 - - - +
159A LEU* 1.3 68.0 + - - +
160A GLU* 3.9 36.6 + - + +
163A SER* 5.3 0.3 - - - -
187A PHE* 3.7 26.1 - - + -
190A ARG* 3.5 23.1 - - - +
192A ILE* 3.8 33.7 - - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.8 28.0 - - + -
136A SER* 3.9 10.5 - - - +
139A SER 4.1 2.6 - - - +
140A PRO* 3.3 2.5 - - - +
141A SER* 3.0 39.7 + - - +
143A MSE 3.8 22.0 - - + -
157A LEU* 4.0 14.1 - - + +
158A LEU* 1.3 79.1 - - - +
160A GLU* 1.3 64.7 + - - +
163A SER* 3.7 11.0 - - - +
165A TYR* 3.7 36.8 - - + -
179A ILE* 4.0 16.2 - - + -
197A ARG* 4.1 8.5 - - - +
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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