Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 5F4T
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 VAL 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 4.0 0.4 - - - -
139A CYS 4.0 0.2 + - - -
140A GLY* 1.3 79.5 - - - +
142A MET* 1.3 61.9 + - - +
143A LEU* 4.0 23.5 + - + +
158A ALA* 4.6 6.3 - - + -
159A CYS 3.2 7.9 - - - +
160A ARG* 4.3 24.7 - - + +
161A LYS 5.7 0.9 - - - +
186A TRP* 3.7 5.2 - - - -
190A SER* 4.2 1.6 + - - -
241A SER* 4.8 10.1 - - - +
242A PRO 4.4 10.8 - - - +
243A ALA* 3.0 37.2 + - - +
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Residues in contact with MET 142 (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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136A PRO* 3.6 27.6 - - + -
137A ASN* 3.2 19.0 - - - +
141A VAL* 1.3 73.1 - - - +
143A LEU* 1.3 66.2 + - - +
144A GLN* 3.3 42.8 + - + +
157A HIS 3.1 4.2 - - - +
159A CYS* 2.9 39.7 + - + +
186A TRP* 3.5 34.5 - - + +
189A ALA* 4.0 29.8 - - + +
190A SER* 3.8 7.4 - - - +
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Residues in contact with LEU 143 (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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141A VAL* 4.0 15.9 + - + +
142A MET* 1.3 72.9 - - - +
144A GLN* 1.3 59.5 + - - +
156A VAL* 3.7 22.0 - - + -
157A HIS 3.6 3.4 - - - +
158A ALA* 4.1 23.8 - - + +
190A SER* 3.3 12.7 + - - +
191A GLU* 3.2 56.1 + - + +
192A GLY* 4.5 4.7 - - - -
237A SER* 4.3 15.7 - - - +
238A VAL 5.8 1.8 - - - +
240A SER* 6.1 0.7 - - - +
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Residues in contact with GLN 144 (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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79A ASP* 4.6 8.2 + - + +
129A PHE* 4.4 6.1 - - - -
133A ALA* 2.6 27.3 + - - +
134A TYR* 3.9 4.1 - - - -
135A CYS* 3.0 24.5 + - - -
136A PRO* 4.8 0.2 - - - +
142A MET* 3.3 31.6 + - + +
143A LEU* 1.3 72.1 - - - +
145A THR* 1.3 69.0 + - - +
146A LEU* 3.2 24.6 + - + +
156A VAL* 4.4 1.3 - - - -
157A HIS* 2.9 42.3 + - + +
159A CYS* 3.8 10.4 - - - -
189A ALA 4.9 2.7 - - - +
191A GLU* 4.6 0.7 - - - -
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Residues in contact with THR 145 (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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79A ASP* 4.0 16.6 - - - +
80A GLU* 4.8 5.0 + - + +
144A GLN* 1.3 72.0 - - - +
146A LEU* 1.3 71.1 + - - +
147A ILE* 5.2 3.1 - - + +
154A LYS* 4.1 31.2 - - + +
155A GLU 3.7 8.1 - - - +
156A VAL* 4.2 9.1 - - + +
191A GLU* 2.4 43.6 + - - -
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Residues in contact with LEU 146 (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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77A VAL* 3.5 22.4 - - + -
78A VAL 3.3 13.5 - - - +
79A ASP* 4.5 1.1 - - + -
129A PHE* 3.5 24.9 - - + -
134A TYR* 3.7 26.7 - - + -
144A GLN* 3.2 24.2 + - + +
145A THR* 1.3 80.6 - - - +
147A ILE* 1.3 63.1 + - - +
148A TRP 4.1 0.6 + - - -
153A LYS 3.9 0.3 - - - +
154A LYS* 3.4 5.2 - - - +
155A GLU* 2.9 44.3 + - + +
157A HIS* 3.7 22.7 - - + -
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Residues in contact with ILE 147 (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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22A CYS* 5.6 0.9 - - + -
25A CYS* 4.3 13.2 - - + +
77A VAL* 3.4 6.7 - - - -
78A VAL* 2.8 44.3 + - + +
79A ASP 4.5 1.8 - - - -
80A GLU* 3.9 37.0 - - + +
83A LEU* 4.0 22.2 - - + -
145A THR* 5.2 3.1 - - + -
146A LEU* 1.3 77.3 - - - +
148A TRP* 1.3 73.6 + - - +
149A CYS* 3.4 4.4 + - - -
152A CYS* 4.1 15.7 - - - +
153A LYS 3.5 8.7 - - - +
154A LYS* 4.3 21.5 - - + +
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Residues in contact with TRP 148 (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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75A MET 4.0 18.8 - - - -
76A GLY* 3.6 17.0 - - - -
77A VAL* 4.5 11.9 - - + +
147A ILE* 1.3 70.6 - - - +
149A CYS* 1.3 56.6 + - - +
150A LYS* 3.4 4.9 - - + +
151A ASN* 3.2 26.9 - - - +
152A CYS* 2.8 32.3 + - - -
153A LYS* 2.8 22.5 + - + +
154A LYS 5.1 0.2 - - - -
155A GLU* 2.3 51.2 + - + -
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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