Contacts of the strand formed by residues 104 - 109 (chain D) in PDB entry 4L28
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 GLU 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.7 2.8 - - - +
91D ARG* 3.1 42.0 + - + +
103D CYS* 1.3 71.8 - - - +
105D LEU* 1.3 58.0 + - - +
106D LEU* 3.5 24.0 + - + +
367D GLY 5.6 0.8 - - - +
368D GLN 2.9 15.0 + - - +
369D ARG* 2.9 38.6 + - + +
370D CYS 2.7 33.1 + - - +
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Residues in contact with LEU 105 (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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91D ARG* 3.9 1.2 - - - +
92D ILE* 2.9 64.5 + - + +
95D ILE* 5.3 0.4 - - + -
96D GLY* 4.4 11.4 - - - +
101D LEU* 4.2 28.5 - - + -
103D CYS* 3.5 4.1 + - - +
104D GLU* 1.3 72.6 - - - +
106D LEU* 1.3 65.9 + - - +
354D VAL* 4.9 17.5 - - + -
357D ALA* 4.5 5.6 - - + -
358D VAL* 5.0 4.5 - - + -
370D CYS* 3.4 33.9 - - + +
372D VAL* 4.0 17.3 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.6 35.2 - - + -
89D MET* 3.9 19.5 - - + -
90D VAL 3.8 1.3 - - - +
91D ARG* 3.8 20.9 - - + +
92D ILE* 4.6 2.7 - - - -
104D GLU* 3.5 29.2 - - + +
105D LEU* 1.3 79.9 - - - +
107D ALA* 1.3 55.6 + - - +
244D CYS* 4.4 1.8 - - - -
369D ARG* 3.7 28.0 - - - +
370D CYS 2.6 15.2 + - - +
371D VAL* 3.3 9.6 - - + -
372D VAL* 2.7 36.3 + - - +
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Residues in contact with ALA 107 (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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89D MET* 3.4 5.0 - - - -
90D VAL 2.9 40.9 + - - +
92D ILE* 3.9 19.1 - - + -
106D LEU* 1.3 75.5 - - - +
108D LYS* 1.3 59.5 + - - +
109D CYS* 3.4 10.7 + - - -
344D LEU* 4.5 1.6 - - + -
354D VAL* 6.3 0.4 - - + -
372D VAL* 3.5 7.4 - - + -
374D LEU* 3.8 29.2 - - + -
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Residues in contact with LYS 108 (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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87D THR* 2.7 37.7 + - - +
88D PRO 3.9 5.4 - - - +
89D MET* 4.0 15.1 - - + -
106D LEU 4.2 0.2 - - - -
107D ALA* 1.3 68.7 - - - +
109D CYS* 1.3 58.4 + - - +
110D GLU* 3.0 25.4 + - - +
121D ARG* 4.4 3.6 - - - +
236D THR* 4.5 4.7 - - + -
239D GLU* 3.0 28.0 + - - +
240D ILE* 4.0 17.5 - - + -
243D GLN* 2.9 23.8 + - - +
371D VAL* 4.6 4.5 - - + -
372D VAL 2.8 16.0 + - - +
373D ILE* 3.7 20.8 - - + +
374D LEU* 3.3 20.0 + - - +
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Residues in contact with CYS 109 (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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87D THR* 3.2 19.4 - - - -
88D PRO* 3.0 17.3 + - + +
90D VAL* 3.7 28.3 - - - -
107D ALA* 3.9 7.9 - - - -
108D LYS* 1.3 67.4 - - - +
110D GLU* 1.3 63.0 + - - +
111D PHE* 3.2 19.9 + - + -
112D PHE* 3.7 29.3 + - + -
344D LEU* 3.8 22.9 - - - -
374D LEU* 4.3 9.2 - - - -
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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