Contacts of the helix formed by residues 110 - 124 (chain X) 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 SER 110 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74V ASP* 5.6 8.7 - - - -
108X GLU* 3.6 3.2 - - - +
109X PHE* 1.3 76.5 - - - +
111X PRO* 1.3 63.8 - - - +
112X ARG* 3.2 5.6 - - - -
113X VAL* 3.1 16.6 + - - +
114X VAL* 3.0 22.4 + - - +
131X LEU* 6.5 0.2 - - - -
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Residues in contact with PRO 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T LYS 6.1 1.6 - - - +
109X PHE 3.7 5.6 - - - +
110X SER* 1.3 66.3 - - - +
112X ARG* 1.3 58.7 + - - +
113X VAL 2.9 11.3 + - - -
114X VAL* 4.1 7.7 - - + +
115X ARG* 3.2 22.0 + - - +
131X LEU* 6.1 3.1 - - + -
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Residues in contact with ARG 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70V PRO* 6.3 0.9 - - + -
71V LEU* 3.8 31.5 - - + +
110X SER* 3.2 4.4 - - - -
111X PRO* 1.3 77.0 - - - +
113X VAL* 1.3 58.5 + - + +
115X ARG* 3.7 14.0 - - - +
116X GLU* 4.8 1.7 + - - +
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Residues in contact with VAL 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71V LEU* 4.5 18.4 - - + +
74V ASP* 5.7 5.2 - - + -
75V GLU* 5.8 1.6 - - + +
86X ALA* 3.9 24.9 - - + +
87X SER* 4.1 6.5 - - - +
110X SER* 3.1 17.2 + - - +
111X PRO 2.9 0.6 - - - -
112X ARG* 1.3 80.9 - - + +
114X VAL* 1.3 56.5 + - - +
115X ARG 2.9 4.7 - - - -
116X GLU* 2.8 25.0 + - - +
117X LEU 3.1 7.8 + - - -
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Residues in contact with VAL 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125T THR* 6.1 3.6 - - - -
86X ALA 4.5 1.7 + - - -
108X GLU* 4.9 14.2 - - + +
110X SER 3.0 15.9 + - - +
111X PRO* 4.1 9.2 - - + +
113X VAL* 1.3 74.7 - - - +
115X ARG* 1.3 62.0 + - - +
117X LEU* 3.5 12.0 - - + +
118X LEU* 2.9 24.9 + - - +
130X LEU 6.1 0.2 - - - -
131X LEU* 4.8 18.4 - - + +
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Residues in contact with ARG 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285T ASP* 5.2 13.6 - - + +
111X PRO 3.2 17.6 + - - +
112X ARG* 3.7 14.6 - - - +
114X VAL* 1.3 77.5 - - - +
116X GLU* 1.3 59.9 + - + +
118X LEU* 3.5 16.3 - - - +
119X LEU* 4.0 4.2 + - - +
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Residues in contact with GLU 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285T ASP* 5.3 13.0 - - + -
286T GLU* 6.1 1.8 - - + +
87X SER* 3.7 22.6 - - - +
112X ARG 5.5 0.9 - - - +
113X VAL* 2.8 10.9 + - - +
115X ARG* 1.3 77.0 - - + +
117X LEU* 1.3 64.0 + - - +
118X LEU 3.3 0.7 - - - -
119X LEU* 3.6 10.6 + - - +
120X VAL* 3.6 13.9 + - - +
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Residues in contact with LEU 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X ALA* 5.6 4.0 - - + +
86X ALA 3.4 22.7 - - - +
87X SER 3.8 11.6 + - - +
88X GLY* 4.9 2.5 - - - +
113X VAL 3.1 4.8 + - - -
114X VAL* 3.2 15.5 + - - +
116X GLU* 1.3 74.5 - - - +
118X LEU* 1.3 53.9 + - - +
120X VAL* 3.0 7.8 + - - +
121X ALA* 2.8 36.3 + - - +
129X PRO* 5.5 8.1 - - + -
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Residues in contact with LEU 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X VAL 2.9 11.2 + - - +
115X ARG* 3.5 15.7 - - - +
117X LEU* 1.3 75.4 - - - +
119X LEU* 1.3 57.8 + - - +
121X ALA* 3.1 6.1 + - - +
122X GLN* 2.8 32.4 + - - +
129X PRO* 5.4 5.2 - - - -
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Residues in contact with LEU 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282T GLY 5.8 1.3 - - - +
283T SER* 4.9 17.7 - - - -
115X ARG 4.0 3.5 + - - +
116X GLU* 3.6 13.5 + - - +
117X LEU 3.3 0.2 - - - -
118X LEU* 1.3 80.5 - - - +
120X VAL* 1.3 63.0 + - - +
122X GLN* 3.5 11.6 + - - +
123X ARG* 3.6 12.5 + - - +
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Residues in contact with VAL 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X VAL* 4.9 17.9 - - + -
87X SER 4.6 7.9 - - - +
88X GLY* 4.8 10.3 - - - +
92X SER* 5.5 4.3 - - - -
116X GLU 3.6 8.7 + - - +
117X LEU* 3.0 12.8 + - - +
119X LEU* 1.3 79.0 - - - +
121X ALA* 1.3 62.3 + - - +
122X GLN 3.5 0.3 + - - -
123X ARG* 3.6 5.9 + - - +
124X ARG* 3.5 21.8 + - - +
127X ILE* 5.8 0.4 - - - -
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Residues in contact with ALA 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T LEU* 6.6 0.4 - - - -
117X LEU* 2.8 15.2 + - + +
118X LEU* 3.8 4.9 - - - +
120X VAL* 1.3 74.0 - - - +
122X GLN* 1.3 65.5 + - - +
124X ARG 3.1 20.9 - - - +
125X PRO* 5.2 0.2 - - - +
127X ILE* 4.0 29.1 - - + +
129X PRO* 4.2 22.0 - - + -
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Residues in contact with GLN 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T LEU* 6.3 2.9 - - - -
118X LEU 2.8 15.1 + - - +
119X LEU* 3.8 9.2 - - - +
120X VAL 3.3 0.2 - - - -
121X ALA* 1.3 79.1 - - - +
123X ARG* 1.3 63.8 + - - +
124X ARG* 3.1 3.3 + - - -
125X PRO* 4.9 0.5 - - - +
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Residues in contact with ARG 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X VAL* 4.5 23.0 - - + +
36X PHE* 6.1 4.0 - - + -
119X LEU 3.6 8.1 + - - +
120X VAL* 3.6 8.6 + - - +
121X ALA 3.4 0.4 - - - -
122X GLN* 1.3 78.2 - - - +
124X ARG* 1.3 57.3 + - + +
125X PRO 4.2 1.1 - - - -
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Residues in contact with ARG 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X LEU* 6.2 4.0 - - + -
33X VAL* 6.3 0.9 - - + -
95X SER* 5.1 9.4 - - - -
120X VAL 3.5 15.2 + - - +
121X ALA* 3.1 17.9 + - - +
122X GLN 3.1 3.9 - - - -
123X ARG* 1.3 79.0 - - + +
125X PRO* 1.4 60.8 - - - +
126X ASN* 3.1 13.1 + - + +
127X ILE* 3.2 20.6 + - + +
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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