Contacts of the helix formed by residues 125 - 134 (chain x) in PDB entry 5GJQ
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 VAL 125 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121x CYS 4.2 0.9 - - - +
122x ILE* 3.5 15.7 - - - +
123x ARG 2.9 6.7 + - - +
124x SER* 1.3 76.6 - - - +
126x PRO* 1.4 53.1 - - - +
128x LEU* 2.7 51.7 + - + +
129x LYS* 3.0 5.8 + - - +
245x PHE* 5.7 0.7 - - + -
246x PHE* 3.8 23.3 - - + -
322x TYR* 3.4 37.7 - - + -
420x GLN* 4.1 3.8 - - - +
478x LEU* 3.8 28.7 - - + -
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Residues in contact with PRO 126 (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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123x ARG 4.9 0.4 - - - +
124x SER 2.6 24.2 - - - +
125x VAL* 1.4 74.6 - - - -
127x GLU* 1.3 77.8 + - - +
128x LEU 2.9 1.4 + - - -
129x LYS* 2.9 31.5 + - + +
130x ASP* 3.1 20.7 - - - +
322x TYR* 4.1 8.7 - - + +
420x GLN* 5.1 3.4 - - - +
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Residues in contact with GLU 127 (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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125x VAL 3.2 0.6 + - - -
126x PRO* 1.3 87.0 - - - +
128x LEU* 1.3 61.2 + - - +
130x ASP* 4.1 13.1 - - - +
131x ALA* 4.0 8.8 + - - +
217x ILE* 5.9 1.2 - - - +
241x LEU* 4.3 14.8 - - - +
245x PHE* 3.4 37.1 - - + -
321x ALA* 6.2 0.2 - - + -
322x TYR* 2.9 32.0 + - + +
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Residues in contact with LEU 128 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122x ILE* 3.1 42.8 - - + +
125x VAL* 2.7 30.2 + - + +
127x GLU* 1.3 71.6 - - - +
129x LYS* 1.3 65.8 + - - +
131x ALA* 2.7 24.9 - - + +
132x LEU* 3.6 9.2 + - + +
159x PHE* 6.0 1.1 - - + -
207x MET* 4.8 2.2 - - - -
210x LEU* 4.6 13.0 - - + -
214x LEU* 3.3 30.1 - - + -
241x LEU* 4.5 11.4 - - + +
242x ILE* 5.1 2.9 - - + -
246x PHE* 4.1 26.2 - - + -
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Residues in contact with LYS 129 (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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122x ILE 5.6 0.2 - - - +
123x ARG* 3.0 56.7 - - - +
124x SER* 5.2 2.1 - - - +
125x VAL 3.0 9.4 + - - +
126x PRO* 2.9 26.7 + - + +
128x LEU* 1.3 70.0 - - - +
130x ASP* 1.3 57.1 + - - +
131x ALA 2.8 0.5 + - - -
132x LEU* 2.5 47.9 + - - +
133x LYS* 3.2 12.6 + - + +
159x PHE* 4.1 16.2 - - + -
163x ASP* 4.2 14.9 + - - +
441x ARG* 5.2 7.3 - - - +
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Residues in contact with ASP 130 (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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126x PRO* 3.1 19.9 + - - +
127x GLU* 4.1 13.2 - - - +
129x LYS* 1.3 77.7 - - - +
131x ALA* 1.3 59.7 + - - +
133x LYS* 3.2 17.7 + - - +
134x ARG* 2.9 54.9 + - - +
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Residues in contact with ALA 131 (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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127x GLU 4.0 2.1 + - - +
128x LEU 2.7 19.8 + - - +
129x LYS 2.8 2.0 + - - -
130x ASP* 1.3 75.9 - - - +
132x LEU* 1.3 55.7 + - - +
134x ARG* 2.5 35.8 - - - +
135x TYR* 3.8 1.0 - - - +
214x LEU* 3.3 41.5 - - + +
215x GLU 6.0 0.4 - - - +
241x LEU* 4.1 18.2 - - + -
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Residues in contact with LEU 132 (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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122x ILE* 6.1 0.4 - - + -
128x LEU* 4.1 13.0 - - + +
129x LYS* 2.5 22.5 + - - +
131x ALA* 1.3 68.7 - - - +
133x LYS* 1.3 61.7 + - + +
134x ARG 2.9 6.5 + - - -
135x TYR* 3.7 12.1 + - + +
152x THR* 3.8 22.7 - - + +
155x LEU* 4.1 15.9 - - + +
156x ARG* 3.6 35.5 - - - +
159x PHE* 3.6 40.8 - - + -
210x LEU* 3.9 25.6 - - + -
214x LEU* 4.4 8.5 - - + -
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Residues in contact with LYS 133 (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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129x LYS* 3.2 15.4 + - + +
130x ASP* 3.2 18.6 + - - +
132x LEU* 1.3 78.5 - - + +
134x ARG* 1.3 58.2 + - + +
135x TYR 4.0 2.4 + - - +
156x ARG* 5.5 2.5 - - - -
160x ASP* 3.9 37.6 + - - +
163x ASP* 4.7 18.5 + - - +
164x LYS* 5.7 3.4 - - - +
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Residues in contact with ARG 134 (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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130x ASP* 2.9 45.0 + - - +
131x ALA* 2.5 20.9 - - - +
132x LEU 2.9 0.6 - - - -
133x LYS* 1.3 78.9 - - + +
135x TYR* 1.3 62.3 + - - +
214x LEU* 5.3 0.5 - - - +
217x ILE* 4.1 24.5 - - - +
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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