Contacts of the strand formed by residues 140 - 145 (chain D) in PDB entry 4JF7
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 LEU 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D PHE* 3.7 51.4 - - + -
136D GLU 3.7 12.1 - - - +
137D GLY* 3.6 26.6 + - - +
138D ARG 3.5 2.9 - - - +
139D ASN* 1.3 80.8 - - - +
141D THR* 1.3 62.9 + - - +
469D LEU* 3.9 26.5 - - + -
483D THR* 4.2 3.1 - - + -
502D ILE* 4.1 12.1 - - + +
509D ILE* 4.0 20.3 - - + +
510D SER* 4.2 2.1 - - - -
562D VAL* 4.1 10.8 - - + -
563D THR 3.5 10.1 - - - +
564D LEU* 4.0 6.3 - - + -
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Residues in contact with THR 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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139D ASN 4.9 1.3 - - - -
140D LEU* 1.3 77.6 + - - +
142D LEU* 1.3 66.4 + - - +
143D GLY* 5.8 0.2 - - - -
502D ILE* 3.8 5.6 - - - -
509D ILE 5.0 1.2 + - - -
510D SER* 3.3 17.9 + - - -
562D VAL* 3.7 2.9 - - - -
563D THR* 2.9 51.8 + - - +
565D SER* 3.4 16.2 - - - +
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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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141D THR* 1.3 80.1 + - - +
143D GLY* 1.3 63.2 + - - +
485D THR* 4.3 0.7 - - - +
500D MET* 3.3 42.6 - - + +
501D TYR* 3.9 4.7 - - - +
502D ILE* 3.7 23.3 - - + -
510D SER* 2.8 21.6 + - - +
511D SER* 4.3 0.4 - - - -
512D GLN* 4.1 28.9 + - + +
541D TYR* 3.5 24.2 - - - +
560D ARG* 3.8 22.4 - - - +
561D GLN 4.0 0.7 - - - -
562D VAL* 4.5 7.4 - - + -
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Residues in contact with GLY 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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141D THR 3.6 2.0 + - - -
142D LEU* 1.3 73.3 - - - +
144D PRO* 1.3 68.3 - - - +
560D ARG* 2.8 37.7 + - - -
561D GLN* 2.9 22.4 + - - -
563D THR* 4.3 13.6 - - - +
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Residues in contact with PRO 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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143D GLY* 1.3 87.2 - - - +
145D LEU* 1.3 69.0 + - - +
146D LEU* 3.5 18.5 + - + +
560D ARG* 3.4 12.4 - - - +
561D GLN* 4.5 1.6 + - + -
563D THR* 6.0 0.2 - - + -
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Residues in contact with LEU 145 (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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143D GLY 3.8 1.0 + - - -
144D PRO* 1.3 76.7 - - - +
146D LEU* 1.3 64.5 + - - +
147D ASN 4.3 0.3 + - - -
500D MET* 4.2 1.6 - - + -
514D PHE* 4.3 19.7 - - + -
558D PHE* 3.7 45.5 - - + -
559D ILE 3.5 10.5 - - - +
560D ARG* 3.6 40.1 - - + +
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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