Contacts of the helix formed by residues 128 - 137 (chain G) in PDB entry 5HJD
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 THR 128 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E ARG* 4.8 0.9 - - - -
92G LYS* 6.1 3.6 - - + -
93G GLU* 3.4 34.3 + - + +
127G PRO* 1.3 78.8 - - - +
129G GLU* 1.3 58.7 + - - +
130G ASP* 3.8 5.9 + - - +
131G PHE* 3.3 24.2 + - - +
132G ARG* 3.0 26.2 + - - +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E GLU* 3.6 14.1 - - + +
132E ARG* 4.1 21.5 + - - +
133E ARG* 3.6 35.6 + - - +
128G THR* 1.3 74.7 - - - +
130G ASP* 1.3 61.9 + - - +
132G ARG* 3.4 12.1 + - + +
133G ARG* 3.0 43.1 + - - +
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Residues in contact with ASP 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G LYS 5.4 2.8 - - - +
128G THR* 3.3 5.4 + - - +
129G GLU* 1.3 77.3 - - - +
131G PHE* 1.3 65.9 + - - +
133G ARG* 3.1 34.3 + - - +
134G LYS* 3.5 32.2 + - - +
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Residues in contact with PHE 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G PHE* 3.9 20.0 - - + -
89G PHE* 3.9 15.7 - - + -
90G LYS* 3.8 25.6 - - - +
91G ASN* 3.1 39.7 - - - +
92G LYS 6.1 0.2 - - - +
93G GLU* 6.1 1.1 - - + -
124G PHE* 3.9 19.7 - + - -
127G PRO* 3.9 13.0 - - + -
128G THR* 3.3 22.0 + - - +
130G ASP* 1.3 80.0 + - - +
132G ARG* 1.3 59.7 + - - +
134G LYS* 3.4 10.2 - - + +
135G LEU* 3.0 63.7 + - + +
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Residues in contact with ARG 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E CYS* 3.3 34.6 - - - +
126E ASN* 5.6 0.2 - - - +
127E PRO* 3.4 24.4 + - - +
128E THR* 4.6 0.6 - - - +
129E GLU* 3.7 29.7 + - - +
132E ARG* 3.3 42.1 - - - +
5G CYS* 4.5 1.8 - - - -
7G VAL* 4.2 12.8 - - + -
127G PRO* 4.5 6.3 - - + -
128G THR 3.0 18.3 + - - +
129G GLU* 3.5 9.1 + - - +
130G ASP 3.2 0.2 - - - -
131G PHE* 1.3 75.6 - - - +
133G ARG* 1.3 63.1 + - - +
135G LEU* 3.1 13.9 + - - +
136G LEU* 2.9 48.3 + - + +
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Residues in contact with ARG 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E GLU* 2.3 40.5 + - - +
129G GLU* 3.0 37.3 + - - +
130G ASP* 3.1 33.0 + - - +
132G ARG* 1.3 81.3 - - - +
134G LYS* 1.3 60.2 + - + +
136G LEU* 3.8 7.4 - - - +
137G LYS* 3.0 45.9 + - + +
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Residues in contact with LYS 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G HIS* 3.3 44.7 - - + +
47G PHE* 4.1 9.7 - - + +
90G LYS* 3.9 33.9 - - + +
130G ASP* 3.5 32.9 + - - +
131G PHE* 3.4 15.9 - - + +
133G ARG* 1.3 82.8 - - + +
135G LEU* 1.3 61.7 + - - +
137G LYS* 3.3 20.0 + - - +
138G ALA 3.9 1.0 + - - -
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E SER* 3.2 19.6 + - - -
7G VAL* 3.7 31.4 - - + -
9G VAL* 3.7 12.2 - - + +
47G PHE* 3.6 26.9 - - + -
124G PHE* 3.7 25.8 - - + -
127G PRO* 4.4 3.4 - - + -
131G PHE* 3.0 59.1 + - + +
132G ARG* 3.4 12.1 - - - +
134G LYS* 1.3 75.9 - - - +
136G LEU* 1.3 61.7 + - - +
138G ALA* 3.5 11.4 + - - +
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Residues in contact with LEU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 4.4 12.2 + - - +
3E SER* 3.8 11.4 - - - +
4E SER* 3.7 37.0 - - - +
5E CYS* 4.1 4.7 - - + +
126E ASN* 4.3 8.1 - - + +
7G VAL* 4.2 8.7 - - + -
132G ARG* 2.9 62.2 + - + +
133G ARG* 3.8 6.5 - - - +
135G LEU* 1.3 73.0 - - - +
137G LYS* 1.3 60.6 + - - +
138G ALA 3.1 12.7 + - - +
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Residues in contact with LYS 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ASN* 5.4 0.7 + - - +
46G HIS* 3.2 50.8 + - + +
133G ARG* 3.0 38.9 + - + +
134G LYS* 3.7 12.6 - - - +
135G LEU 3.3 1.0 - - - -
136G LEU* 1.3 76.8 - - - +
138G ALA* 1.3 60.8 + - - +
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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