Contacts of the helix formed by residues 98 - 107 (chain w) 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 GLY 98 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90g ALA* 2.5 13.5 - - - -
21w ALA* 5.9 2.6 - - - +
95w GLY 5.2 0.9 - - - -
96w PRO 2.6 9.9 + - - -
97w GLY* 1.3 64.2 - - - -
99w GLN* 1.3 59.8 + - - -
101w ALA* 2.8 29.5 + - - +
102w LEU* 2.8 21.1 + - - +
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Residues in contact with GLN 99 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88g ASP* 3.3 33.4 - - + +
89g PRO* 4.9 0.4 - - - -
90g ALA* 1.5 57.6 - - + +
91g ALA 4.2 0.2 - - - +
97w GLY 2.9 0.9 + - - +
98w GLY* 1.3 67.0 - - - -
100w ALA* 1.3 57.6 + - - +
103w ARG* 2.4 41.7 + - + +
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Residues in contact with ALA 100 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57w PRO* 3.3 28.7 - - + -
60w ALA* 3.6 15.4 - - + +
61w MET* 6.0 0.4 - - - -
97w GLY 2.9 14.3 + - - +
99w GLN* 1.3 75.1 - - - +
101w ALA* 1.3 54.4 + - - +
104w ALA* 2.4 43.8 + - - +
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Residues in contact with ALA 101 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19w ILE* 4.7 19.5 - - + -
21w ALA* 6.5 1.8 - - + -
26w THR* 6.6 0.2 - - - -
27w PHE 5.8 2.9 - - - +
60w ALA* 4.6 3.6 - - + +
83w ILE* 6.4 0.4 - - + -
97w GLY* 3.5 3.2 - - - -
98w GLY* 2.8 30.4 + - - +
100w ALA* 1.3 81.2 - - - +
102w LEU* 1.3 67.4 + - + +
104w ALA* 3.0 11.6 + - - +
105w LEU* 3.5 5.7 + - - +
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Residues in contact with LEU 102 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89g PRO* 5.3 9.9 - - + -
90g ALA 6.2 0.2 - - - +
19w ILE* 5.6 3.3 - - + +
81w VAL* 5.0 17.0 - - + -
83w ILE* 6.2 3.6 - - + -
98w GLY 2.8 8.6 + - - +
101w ALA* 1.3 79.5 - - + +
103w ARG* 1.3 60.5 + - - +
105w LEU* 3.7 5.7 + - - +
106w ALA* 3.4 18.6 + - - +
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Residues in contact with ARG 103 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87g TYR 5.0 8.3 - - - +
88g ASP* 5.3 0.2 - - - -
89g PRO* 5.0 13.3 - - + +
99w GLN* 2.4 36.3 + - + +
102w LEU* 1.3 75.0 - - - +
104w ALA* 1.3 68.9 + - - +
106w ALA* 2.8 17.9 + - - +
107w ARG* 2.9 14.0 + - - +
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Residues in contact with ALA 104 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60w ALA 4.2 14.8 - - - +
63w ALA* 4.8 3.8 - - + +
64w ALA* 4.6 13.2 - - + +
99w GLN 3.5 0.2 + - - -
100w ALA* 2.4 33.0 + - - +
101w ALA* 3.0 4.7 + - - +
103w ARG* 1.3 75.8 - - - +
105w LEU* 1.3 53.8 + - - +
106w ALA 2.8 0.9 + - - -
107w ARG* 2.7 36.5 + - - +
108w SER* 4.8 1.6 - - - -
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Residues in contact with LEU 105 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64w ALA* 4.2 19.6 - - + +
68w ALA* 5.5 5.2 - - + -
101w ALA 3.5 5.3 + - - +
102w LEU* 4.2 7.0 - - - +
103w ARG 3.5 0.2 - - - -
104w ALA* 1.3 79.0 - - - +
106w ALA* 1.3 58.6 + - - +
108w SER* 3.7 14.2 + - - +
109w GLY 4.9 0.2 - - - -
110w LEU* 3.8 24.5 - - + +
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Residues in contact with ALA 106 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102w LEU 3.4 12.3 + - - +
103w ARG* 2.8 17.4 + - - +
104w ALA 2.8 0.2 + - - -
105w LEU* 1.3 75.2 - - - +
107w ARG* 1.3 50.5 + - - +
108w SER 2.7 24.4 + - - +
110w LEU* 5.4 4.2 - - - +
111w ARG* 5.7 4.7 - - - +
112w ILE* 5.8 9.2 - - + +
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Residues in contact with ARG 107 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103w ARG 2.9 8.3 + - - +
104w ALA* 2.7 20.4 + - - +
106w ALA* 1.3 67.3 - - - +
108w SER* 1.3 62.3 + - - +
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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