Contacts of the strand formed by residues 144 - 148 (chain B) in PDB entry 6E8Z
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 MET 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.8 11.7 - - + -
115B GLY* 3.4 19.7 - - - -
116B ILE 4.1 0.9 - - - -
117B SER* 3.8 35.2 - - - +
133B SER* 3.6 29.2 - - - +
136B ILE* 3.7 34.5 - - + -
137B GLY* 3.6 8.7 - - - -
142B ILE* 3.4 22.2 + - - +
143B PRO* 1.3 72.3 - - - +
145B SER* 1.3 62.2 + - - +
168B CYS* 5.2 0.7 - - - -
169B LYS* 5.3 1.4 + - - +
194B VAL* 3.8 18.9 - - + +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY 2.8 11.7 + - - -
116B ILE* 3.3 7.1 - - - -
117B SER* 2.8 22.0 + - - -
144B MET* 1.3 78.8 + - - +
146B VAL* 1.3 67.0 + - - +
166B ILE* 4.6 0.4 - - - -
167B GLY 3.1 17.5 - - - -
168B CYS* 3.0 30.5 - - - +
173B GLN* 4.2 3.1 - - - +
177B LEU* 3.5 25.3 - - - +
194B VAL* 4.5 1.1 - - - -
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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
----------------------------------------------------------
116B ILE* 3.8 3.8 - - - -
117B SER* 3.3 11.9 - - - +
133B SER* 3.8 11.7 - - - -
145B SER* 1.3 80.6 - - - +
147B LEU* 1.3 60.7 + - - +
148B MET* 4.2 8.5 - - + -
166B ILE* 3.2 9.9 - - - +
167B GLY* 2.8 36.7 + - - +
194B VAL* 3.7 17.0 - - + +
197B VAL* 3.3 35.4 - - + -
198B GLU* 3.4 35.2 - - - +
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Residues in contact with LEU 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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14B TRP* 4.0 26.7 + - + -
18B ILE* 5.0 0.4 - - + -
116B ILE* 3.8 5.8 - - + -
117B SER 2.9 8.7 + - - -
118B LEU* 3.7 33.9 - - + +
120B LYS* 5.5 0.3 - - - +
146B VAL* 1.3 75.5 - - - +
148B MET* 1.3 73.5 + - - +
151B ASN* 4.9 1.6 - - - +
164B THR* 3.3 35.4 - - + +
165B THR 3.4 4.5 - - - +
166B ILE* 4.2 10.3 - - + -
181B MET* 3.8 35.2 - - + -
186B PHE* 4.3 8.5 - - + -
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.7 17.5 - - - +
118B LEU 4.1 1.8 - - - +
119B ILE 3.2 29.2 - - - +
120B LYS* 3.7 32.8 - - + -
146B VAL* 4.3 10.8 - - + -
147B LEU* 1.3 86.2 - - - +
149B GLY* 1.3 54.9 + - - +
151B ASN* 5.9 0.2 - - - +
164B THR* 3.0 6.2 + - - -
165B THR* 2.7 42.0 + - - +
197B VAL* 3.7 37.9 - - + +
198B GLU* 4.4 17.9 - - + +
201B GLY* 5.7 2.7 - - - +
256B CYS* 3.7 7.6 - - + +
260B ASP* 5.7 0.9 - - - +
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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