Contacts of the helix formed by residues 120 - 128 (chain Z) in PDB entry 5L4K
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 ARG 120 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87Z THR* 3.2 33.1 + - - +
89Z MET* 5.1 16.9 - - - +
117Z GLU* 4.5 6.3 - - - +
119Z LYS* 1.3 84.1 - - + +
121Z PHE* 1.3 77.0 + - - +
122Z ALA 3.6 0.9 - - - -
123Z ALA* 4.1 5.1 + - - +
124Z ASP* 3.0 50.3 + - - +
129Z LEU* 6.0 0.8 - - - +
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Residues in contact with PHE 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z ARG* 3.4 45.3 - - + -
87Z THR* 3.8 12.6 - - + -
88Z SER 5.8 3.8 - - - -
89Z MET* 6.0 4.7 - - - -
92Z VAL* 5.2 5.8 - - + -
96Z LEU* 5.0 5.8 - - + -
115Z PRO 3.9 11.7 - - - -
116Z GLY* 3.9 2.7 - - - -
117Z GLU* 3.6 25.9 + - - +
119Z LYS 3.7 1.0 - - - +
120Z ARG* 1.3 104.6 - - - +
122Z ALA* 1.3 59.6 + - - +
123Z ALA 3.3 1.8 - - - -
124Z ASP* 3.7 3.4 - - + -
125Z ILE* 2.9 53.0 + - + +
129Z LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Z ASP* 4.3 7.2 - - - +
113Z MET* 5.1 6.7 - - + -
115Z PRO* 5.9 0.2 - - - -
116Z GLY* 3.9 9.6 - - - +
117Z GLU 3.8 5.7 - - - +
118Z ASN* 3.5 34.5 - - - +
119Z LYS 4.4 2.9 - - - +
120Z ARG 3.6 0.4 - - - -
121Z PHE* 1.3 80.0 - - - +
123Z ALA* 1.3 61.5 + - - +
125Z ILE* 3.5 12.6 - - - +
126Z ILE* 3.8 17.3 + - + +
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Residues in contact with ALA 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Z LYS 5.3 4.2 + - - +
120Z ARG* 4.1 7.4 + - - +
121Z PHE 3.3 0.2 - - - -
122Z ALA* 1.3 78.9 - - - +
124Z ASP* 1.3 63.3 + - - +
126Z ILE* 5.6 0.7 - - - -
127Z SER* 2.9 44.7 + - - +
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Residues in contact with ASP 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Z ARG* 3.0 40.2 + - - +
121Z PHE* 3.4 9.7 + - + +
123Z ALA* 1.3 80.0 - - - +
125Z ILE* 1.3 57.4 + - - +
128Z VAL* 2.9 22.7 - - + +
129Z LEU* 2.7 44.9 + - + +
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Residues in contact with ILE 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z ARG* 3.8 26.0 - - - +
96Z LEU* 5.0 3.8 - - + -
110Z TYR* 3.6 22.3 - - + +
115Z PRO* 3.5 40.2 - - + +
116Z GLY 4.1 1.1 - - - +
121Z PHE* 2.9 51.8 + - + +
122Z ALA 3.5 8.7 - - - +
124Z ASP* 1.3 78.4 - - - +
126Z ILE* 1.3 62.5 + - + +
129Z LEU* 4.0 15.3 - - + +
130Z ALA* 3.2 25.8 + - - +
133Z MET* 5.4 0.2 - - + -
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Residues in contact with ILE 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Z LYS* 6.0 1.8 - - - +
110Z TYR* 3.0 52.5 - - + +
112Z ASN 4.6 4.0 - - - +
115Z PRO* 4.3 5.8 - - + -
122Z ALA* 3.8 13.6 + - + +
123Z ALA 3.6 1.4 + - - +
125Z ILE* 1.3 89.3 - - + +
127Z SER* 1.3 68.3 + - - +
128Z VAL 3.4 0.6 + - - -
130Z ALA* 3.6 17.1 - - - +
177Z GLU* 6.1 0.9 - - - +
178Z LYS* 3.8 10.6 + - - +
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Residues in contact with SER 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Z ALA* 2.9 27.6 + - - +
126Z ILE* 1.3 81.8 - - - +
128Z VAL* 1.3 70.1 + - - +
131Z MET* 3.2 23.2 - - - +
178Z LYS* 4.2 3.6 - - - +
181Z ARG* 5.3 5.6 + - - +
185Z LEU* 4.5 6.9 - - - +
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Residues in contact with VAL 128 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Z ALA 4.6 0.2 - - - +
124Z ASP* 2.9 43.7 + - + +
126Z ILE 3.4 0.6 - - - -
127Z SER* 1.3 90.2 - - - +
129Z LEU* 1.3 63.4 + - + +
130Z ALA 3.2 4.9 + - - -
131Z MET* 3.7 11.9 + - + +
132Z THR* 2.9 30.7 + - - +
185Z LEU* 5.2 9.9 - - + -
187Z LEU* 4.9 4.0 - - + +
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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