Contacts of the strand formed by residues 140 - 144 (chain D) in PDB entry 5J0Z
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 ILE 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PRO* 5.6 0.7 - - + -
16D LEU* 3.5 14.4 - - + +
18D VAL* 3.4 30.7 - - + -
72D TRP* 3.9 31.6 - - + -
74D PRO* 5.0 0.9 - - + -
75D GLU 5.9 0.7 - - - +
132D VAL* 4.1 26.1 - - + +
133D ARG 4.2 12.3 - - - +
134D SER* 3.1 19.8 + - - +
135D VAL* 4.7 10.1 - - + -
138D ARG* 3.9 12.6 - - + +
139D ASN* 1.3 101.1 + - - +
141D VAL* 1.3 66.4 + - - +
180D LEU* 3.6 6.6 - - - +
182D SER* 3.6 6.4 - - - -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PRO* 4.7 10.3 - - + -
16D LEU 2.9 14.2 + - - +
17D THR* 3.8 15.9 - - - +
18D VAL* 2.8 35.0 + - - +
139D ASN* 4.6 13.0 - - - +
140D ILE* 1.3 79.2 - - - +
142D LEU* 1.3 74.0 + - - +
143D ALA* 5.2 0.7 - - + -
171D PRO* 4.3 9.2 - - + -
173D ASN* 3.3 26.2 - - - +
180D LEU* 5.0 1.1 - - + -
182D SER* 3.8 3.1 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 3.4 14.4 - - + +
20D THR* 4.0 12.1 - - + -
76D ILE* 3.4 25.4 - - + -
130D LEU* 3.6 28.5 - - + +
131D ILE 3.8 9.6 - - - +
132D VAL* 3.3 25.1 - - + -
141D VAL* 1.3 91.4 - - - +
143D ALA* 1.3 63.0 + - - +
171D PRO* 3.1 14.8 - - - +
182D SER* 3.1 29.1 + - - +
184D LEU* 3.7 22.2 - - + +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 4.3 21.1 - - + +
18D VAL 2.9 8.1 + - - +
19D ASN* 3.5 6.6 - - - +
20D THR* 2.8 35.4 + - - -
141D VAL* 5.2 0.9 - - + -
142D LEU* 1.3 78.3 - - - +
144D VAL* 1.3 60.9 + - - +
169D VAL 4.7 9.0 - - - +
171D PRO* 5.3 1.6 - - + -
184D LEU* 4.0 5.2 - - - -
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASN* 4.5 5.4 - - - +
20D THR* 3.6 5.6 - - - +
143D ALA* 1.3 75.3 - - - +
145D ASP* 1.3 60.9 + - - +
146D LEU* 3.2 41.7 + - + +
149D VAL* 4.0 15.9 - - + -
167D ALA* 4.0 20.4 - - + -
169D VAL* 3.8 27.2 + - + +
184D LEU* 3.7 30.5 - - + -
186D TYR* 4.5 1.8 - - - +
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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