Contacts of the strand formed by residues 148 - 152 (chain J) in PDB entry 6K71
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 PHE 148 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU* 5.1 0.2 - - - -
44J GLN* 3.3 35.0 - - + +
45J ALA* 3.9 0.7 - - - -
46J VAL* 3.5 45.1 - - + -
92J PHE* 6.4 0.2 - + - -
135J LEU* 4.6 8.5 - - + -
138J VAL* 4.5 23.6 - - + -
144J VAL* 3.6 34.3 - - + -
146J SER 4.9 1.3 - - - +
147J ASP* 1.3 78.5 - - - +
149J LEU* 1.3 61.1 + - - +
150J LEU* 5.0 0.2 - - + -
251J ILE* 3.3 3.4 - - - -
252J CYS* 2.7 86.9 + - + +
254J PRO* 5.1 5.8 - - + -
256J VAL* 5.8 2.7 - - + -
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Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU* 5.5 3.1 - - + -
44J GLN 3.5 6.2 + - - +
45J ALA* 3.4 9.5 - - + +
46J VAL 3.0 30.0 + - - +
82J PHE* 5.3 6.1 - - + -
83J LEU* 3.7 29.8 - - + -
86J THR* 4.4 4.7 - - + -
88J VAL* 4.3 11.9 - - + -
148J PHE* 1.3 77.4 - - - +
150J LEU* 1.3 59.2 + - - +
151J VAL* 3.7 6.6 + - + +
161J ILE* 3.7 36.3 - - + -
165J LEU* 4.9 7.2 - - + -
249J ILE* 4.4 11.4 - - + +
250J SER 4.2 1.8 - - - -
251J ILE* 3.6 26.7 - - + -
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Residues in contact with LEU 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J VAL* 3.7 24.7 - - + -
48J VAL* 4.4 17.5 - - + -
131J LEU* 5.2 13.5 - - + -
135J LEU* 4.9 24.2 - - + -
148J PHE* 3.7 2.1 + - + -
149J LEU* 1.3 70.2 - - - +
151J VAL* 1.3 62.9 + - - +
152J TYR* 5.7 6.9 - - + -
248J HIS 4.1 0.9 - - - +
249J ILE* 3.1 23.2 + - - +
250J SER* 2.9 19.4 + - - +
252J CYS* 3.7 19.3 - - + -
269J ARG* 4.7 22.7 + - + +
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Residues in contact with VAL 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J VAL 3.8 8.3 + - - +
47J LEU* 3.5 22.0 - - + +
48J VAL* 3.3 20.7 + - - +
79J THR* 5.2 1.1 - - - +
82J PHE* 4.7 7.0 - - + -
83J LEU* 3.8 22.0 - - + -
149J LEU* 3.7 8.9 + - + +
150J LEU* 1.3 73.4 - - - +
152J TYR* 1.3 72.7 + - - +
155J VAL* 5.1 6.3 - - + -
248J HIS 3.6 15.9 - - - +
249J ILE* 3.4 38.8 - - + +
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Residues in contact with TYR 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J LEU* 3.2 8.8 - - - +
48J VAL* 3.3 26.5 - - + +
49J ALA 4.6 3.8 - - - +
50J ASP* 5.5 0.4 - - - -
51J SER* 3.0 41.0 + - - -
79J THR* 3.8 5.2 + - - -
131J LEU* 4.6 15.8 - - + +
150J LEU* 5.7 8.5 - - + -
151J VAL* 1.3 87.7 - - - +
153J GLY* 1.3 59.9 + - - +
154J ASP* 3.0 22.5 + - + +
155J VAL* 4.0 6.4 + - + +
248J HIS* 4.3 17.5 + + + -
268J THR* 4.7 6.1 - - - +
269J ARG* 4.4 25.5 - - - +
299J ARG* 3.5 43.9 + - + -
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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