Contacts of the strand formed by residues 154 - 159 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C ARG* 3.9 26.9 - - + -
20C GLY 3.8 13.2 - - - -
21C SER* 3.1 49.8 + - - -
25C VAL* 4.1 1.8 - - - +
144C ARG* 4.7 7.9 - - + -
145C LEU 3.2 13.5 - - - +
146C VAL* 4.5 13.2 - - + -
151C PRO 4.6 4.9 - - - -
152C GLY* 3.7 16.3 + - - -
153C GLU* 1.3 74.4 - - - +
155C LEU* 1.3 81.5 + - - +
156C GLU* 3.7 32.8 - - + -
175C PHE* 5.0 1.6 - - - -
188C GLY* 5.8 2.2 - - - -
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.9 11.0 - - + -
19C ARG 3.6 3.8 - - - +
20C GLY* 4.1 2.2 - - - -
25C VAL* 3.8 23.6 - - + +
26C LEU* 3.8 29.8 - - + -
29C LEU* 3.7 32.8 - - + +
33C ALA* 3.9 24.0 - - + +
143C MSE 4.6 0.2 - - - -
144C ARG* 3.2 12.8 - - - +
145C LEU* 2.9 44.9 + - + +
154C TRP* 1.3 83.7 - - - +
156C GLU* 1.3 64.5 + - - +
157C LEU* 5.0 1.8 - - + -
175C PHE* 5.2 1.3 - - + -
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.4 7.4 - - - +
19C ARG* 2.8 40.3 + - + +
142C VAL* 4.2 9.6 - - + -
143C MSE 3.4 5.2 - - - -
144C ARG* 4.0 28.1 + - + -
154C TRP* 3.7 24.7 - - + -
155C LEU* 1.3 78.9 - - - +
157C LEU* 1.3 63.2 + - - +
180C LEU* 5.0 1.7 - - - +
186C PHE 3.4 15.6 - - - +
187C PHE* 3.7 8.4 - - + -
188C GLY* 2.8 33.9 + - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TRP 3.5 2.0 - - - -
18C VAL* 3.6 31.9 - - + -
33C ALA* 4.2 20.9 - - + +
35C VAL* 3.6 31.4 - - + +
142C VAL* 3.7 1.9 - - - +
143C MSE 2.8 51.0 + - + +
145C LEU* 3.8 26.5 - - + -
155C LEU* 5.0 2.5 - - + -
156C GLU* 1.3 75.1 - - - +
158C LEU* 1.3 63.6 + - - +
159C LEU* 3.4 8.9 + - + +
165C TYR* 5.1 5.8 - - + -
167C LEU* 4.4 14.4 - - + -
187C PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TRP* 3.1 50.2 + - + +
35C VAL* 3.7 20.4 - - - +
140C PRO* 5.3 4.3 - - + -
141C SER 3.9 8.3 - - - +
142C VAL* 4.7 1.3 - - + +
157C LEU* 1.3 68.7 - - - +
159C LEU* 1.3 62.5 + - - +
160C GLU* 3.8 7.3 + - + +
163C SER* 5.2 0.2 - - - -
187C PHE* 3.6 34.4 - - + -
190C ARG* 3.4 24.0 - - - +
192C ILE* 3.7 38.1 - - + -
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL* 4.0 17.9 - - + -
136C SER* 3.7 13.9 - - - +
139C SER 4.1 2.4 - - - +
140C PRO* 3.4 2.9 - - - +
141C SER* 2.7 42.0 + - - +
143C MSE 3.8 20.4 - - + -
157C LEU* 3.7 13.5 - - + +
158C LEU* 1.3 78.7 - - - +
160C GLU* 1.3 63.9 + - - +
163C SER* 3.9 7.4 - - - +
165C TYR* 3.8 44.9 - - + +
179C ILE* 4.1 9.2 - - + -
197C ARG* 3.9 17.9 - - - +
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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