Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 4L0D
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG* 2.8 41.8 + - - +
103A CYS* 1.3 74.8 - - - +
105A LEU* 1.3 58.5 + - - +
106A LEU* 3.7 21.9 + - + +
367A GLY 5.6 0.2 - - - +
368A GLN 3.0 14.6 + - - +
369A ARG* 3.1 42.8 + - + +
370A CYS* 2.7 32.9 + - - +
76B ILE* 4.7 2.4 - - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 3.5 4.8 - - - +
92A ILE* 2.7 72.9 + - + +
95A ILE* 5.4 1.1 - - + -
96A GLY* 4.3 19.7 - - - +
101A LEU* 4.5 17.5 - - + -
103A CYS* 3.7 5.6 + - - +
104A GLU* 1.3 74.6 - - - +
106A LEU* 1.3 57.4 + - - +
354A VAL* 5.1 15.7 - - + -
357A ALA* 4.6 6.3 - - + -
358A VAL* 5.4 3.1 - - + -
361A ALA* 5.8 0.2 - - + -
370A CYS* 3.2 28.3 - - + +
372A VAL* 3.9 24.2 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 3.6 22.4 - - + -
90A VAL 3.5 2.2 - - - -
91A ARG* 3.9 9.9 - - + -
92A ILE* 4.5 1.6 - - - -
104A GLU* 3.7 33.2 - - + +
105A LEU* 1.3 78.6 - - - +
107A ALA* 1.3 55.3 + - - +
244A CYS* 4.2 10.5 - - - -
369A ARG* 4.2 12.3 - - + -
370A CYS 2.9 9.2 + - - +
371A VAL* 4.0 21.1 - - + -
372A VAL* 2.7 34.6 + - - +
76B ILE* 3.7 42.8 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO 3.7 0.2 - - - +
89A MET* 3.4 4.7 - - - -
90A VAL* 2.9 37.6 + - + +
92A ILE* 3.8 19.1 - - + -
106A LEU* 1.3 75.9 - - - +
108A LYS* 1.3 60.5 + - - +
109A CYS* 3.5 7.1 + - - -
344A LEU* 4.9 0.2 - - + -
372A VAL* 3.3 8.3 - - + +
374A LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 2.8 37.2 + - - +
88A PRO 3.8 3.1 - - - +
89A MET* 3.8 18.0 - - + -
107A ALA* 1.3 70.6 - - - +
109A CYS* 1.3 60.3 + - - +
110A GLU* 3.3 19.7 + - - +
121A ARG* 4.1 3.8 - - - +
236A THR* 4.6 6.3 - - + -
239A GLU* 2.6 39.7 + - - +
240A ILE* 4.4 11.0 - - + -
243A GLN* 3.0 24.7 + - - +
371A VAL* 4.7 0.4 - - + -
372A VAL 2.8 15.1 + - - +
373A ILE* 4.0 19.4 - - + +
374A LEU* 3.1 23.0 + - - +
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Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 3.1 22.4 - - - +
88A PRO* 3.1 14.2 + - + +
90A VAL* 4.2 16.6 - - - -
107A ALA* 3.8 13.2 - - - -
108A LYS* 1.3 70.6 - - - +
110A GLU* 1.3 57.1 + - - +
111A PHE* 3.3 21.1 - - + -
112A PHE* 3.5 24.9 - - + -
344A LEU* 3.8 29.2 - - - -
374A LEU* 3.9 15.5 - - - -
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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