Contacts of the helix formed by residues 95 - 105 (chain Z) in PDB entry 5JPQ
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 PRO 95 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90Z CYS* 4.8 3.7 - - - +
94Z LYS* 1.4 77.8 - - - +
96Z VAL* 1.3 67.3 + - - +
97Z GLY* 3.2 3.6 - - - +
98Z TYR* 3.1 19.3 + - - +
99Z PHE* 4.1 1.9 + - - +
121Z ILE* 3.1 19.9 - - + +
122Z THR 3.9 2.0 - - - +
123Z ALA* 3.6 35.4 - - - +
124Z SER* 4.3 11.8 - - - +
127Z ASP* 5.1 8.3 - - + -
128Z ALA 5.5 2.0 - - - +
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Residues in contact with VAL 96 (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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90Z CYS* 4.7 12.4 - - + +
95Z PRO* 1.3 70.7 - - - +
97Z GLY* 1.3 56.2 + - - +
99Z PHE* 3.0 10.7 + - - +
100Z VAL* 2.9 27.6 + - + +
118Z PHE* 4.0 30.2 - - + +
119Z LYS 5.4 2.7 - - - +
120Z GLY 5.6 0.7 - - - +
121Z ILE 2.7 16.5 + - - +
122Z THR* 4.4 8.9 - - - +
166Z VAL* 5.2 10.1 - - + +
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Residues in contact with GLY 97 (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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95Z PRO* 3.2 3.8 + - - +
96Z VAL* 1.3 74.0 - - - +
98Z TYR* 1.3 59.6 + - - +
100Z VAL* 4.3 8.1 - - - -
101Z GLU* 3.0 33.3 + - - +
122Z THR 5.2 2.8 + - - -
128Z ALA* 3.2 34.1 + - - +
129Z GLY 5.5 2.5 - - - -
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Residues in contact with TYR 98 (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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18Z ARG* 5.7 3.6 - - - +
94Z LYS* 3.8 21.1 - - + -
95Z PRO 3.1 14.9 + - - +
97Z GLY* 1.3 75.9 - - - +
99Z PHE* 1.3 59.0 + - + +
101Z GLU* 4.4 5.2 + - - +
102Z PRO* 4.5 9.7 - - - +
127Z ASP* 4.4 20.7 - - + +
128Z ALA 5.7 0.2 - - - +
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Residues in contact with PHE 99 (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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52Z PHE* 6.1 7.4 - - - -
55Z LEU* 5.7 9.0 - - + -
88Z HIS* 6.0 6.5 - - + -
90Z CYS* 5.4 9.2 - - + -
95Z PRO 5.0 2.0 - - - +
96Z VAL* 3.0 10.8 + - - +
98Z TYR* 1.3 79.2 - - + +
100Z VAL* 1.3 63.8 + - - +
101Z GLU 3.4 0.4 - - - -
102Z PRO* 4.0 4.4 - - - +
103Z MET* 3.8 14.6 + - - +
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Residues in contact with VAL 100 (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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96Z VAL* 2.9 17.1 + - + +
97Z GLY* 4.2 8.1 - - - +
99Z PHE* 1.3 74.2 - - - +
101Z GLU* 1.3 65.0 + - - +
103Z MET* 3.0 23.9 + - - +
104Z LEU* 3.3 6.8 + - - +
133Z ILE* 5.7 9.9 - - + -
168Z LEU* 5.5 10.1 - - + -
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Residues in contact with GLU 101 (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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97Z GLY 3.0 19.9 + - - +
98Z TYR* 4.5 4.7 - - - +
99Z PHE 3.4 0.4 - - - -
100Z VAL* 1.3 74.3 - - - +
102Z PRO* 1.4 61.3 - - - +
104Z LEU* 3.1 23.8 + - - +
105Z TYR* 3.9 2.9 + - - +
128Z ALA* 4.7 13.7 - - + -
133Z ILE* 6.5 0.7 - - - -
88a PHE* 6.1 3.1 - - + -
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Residues in contact with PRO 102 (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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18Z ARG* 4.3 28.7 - - + +
22Z VAL* 5.0 9.8 - - + +
98Z TYR 4.5 6.3 - - - +
99Z PHE 4.0 7.0 - - - +
100Z VAL 3.5 0.4 - - - -
101Z GLU* 1.4 76.7 - - - +
103Z MET* 1.4 61.8 + - - +
105Z TYR* 3.2 21.8 + - + +
106Z LEU* 3.7 6.4 + - - +
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Residues in contact with MET 103 (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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99Z PHE 3.8 9.8 + - - +
100Z VAL* 3.0 15.8 + - - +
102Z PRO* 1.4 77.7 - - - +
104Z LEU* 1.4 54.8 + - - +
106Z LEU* 3.1 6.4 + - - +
107Z ALA* 2.8 39.9 + - + +
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Residues in contact with LEU 104 (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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100Z VAL 3.3 5.4 + - - +
101Z GLU* 3.1 17.7 + - - +
103Z MET* 1.4 78.8 - - - +
105Z TYR* 1.3 57.6 + - - +
106Z LEU 3.6 0.2 + - - -
107Z ALA* 4.4 6.8 + - - +
108Z PRO* 5.0 6.2 - - - +
137Z LEU* 5.7 9.4 - - + -
141Z MET* 5.5 9.1 - - + +
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Residues in contact with TYR 105 (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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22Z VAL* 4.6 17.5 - - + -
26Z LEU* 5.6 5.4 - - - +
101Z GLU 3.9 1.5 + - - +
102Z PRO* 3.2 15.8 + - + +
103Z MET 3.2 0.4 - - - -
104Z LEU* 1.3 78.3 - - - +
106Z LEU* 1.3 58.1 + - + +
108Z PRO 5.6 0.2 - - - -
109Z PHE* 5.4 4.2 - - - +
299Z VAL* 6.1 5.8 - - + -
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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