Contacts of the helix formed by residues 137 - 144 (chain I) in PDB entry 6D84
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 ALA 137 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135I ASN* 3.1 16.4 + - - +
136I ALA* 1.3 78.8 - - - +
138I GLU* 1.3 65.7 + - - +
139I ILE 3.3 1.6 - - - -
140I THR* 3.3 9.9 + - - +
141I ASP* 3.3 25.7 + - - +
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Residues in contact with GLU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 4.7 7.6 + - - -
134I MET* 3.4 40.3 - - + +
135I ASN* 2.7 22.5 + - - +
137I ALA* 1.3 71.6 - - - +
139I ILE* 1.3 59.5 + - - +
141I ASP* 3.2 11.8 + - + +
142I LYS* 2.9 39.6 + - + +
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Residues in contact with ILE 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I VAL* 4.0 22.9 - - + -
94I SER* 3.3 30.3 - - - +
100I VAL* 5.7 6.7 - - + -
123I VAL* 4.5 0.4 - - + -
125I ALA* 3.7 20.4 - - + -
128I GLN* 4.4 0.4 - - - +
134I MET* 3.7 15.9 - - + -
135I ASN 3.3 19.1 - - - +
137I ALA 3.3 0.2 - - - -
138I GLU* 1.3 78.9 - - - +
140I THR* 1.3 56.8 + - - +
142I LYS* 3.3 7.6 + - - +
143I LEU* 2.9 49.1 + - + +
155I ILE* 3.7 14.8 - - + -
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Residues in contact with THR 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA 3.9 1.4 + - - -
137I ALA* 3.3 12.0 + - - -
138I GLU 3.3 0.4 - - - -
139I ILE* 1.3 77.2 - - - +
141I ASP* 1.3 58.3 + - - +
144I GLY* 2.6 32.2 + - - -
145I LEU* 3.3 27.9 + - + +
146I HIS* 4.7 4.5 - - + +
153I TRP* 3.6 26.4 - - + -
155I ILE* 3.4 29.8 - - - +
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Residues in contact with ASP 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ARG* 5.0 2.8 + - - -
137I ALA* 3.3 15.2 + - - +
138I GLU* 3.2 15.6 + - + +
140I THR* 1.3 82.2 - - - +
142I LYS* 1.3 64.5 + - + +
143I LEU 3.4 0.2 + - - -
144I GLY* 3.5 9.0 + - - -
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Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 3.9 30.7 - - - +
100I VAL* 4.3 24.3 - - + +
101I ASN* 4.8 16.2 + - - +
104I ARG* 2.7 36.0 + - - +
134I MET* 4.8 9.5 - - + +
138I GLU* 2.9 34.8 + - + +
139I ILE* 3.3 6.7 + - - +
141I ASP* 1.3 79.1 - - + +
143I LEU* 1.3 55.2 + - - +
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Residues in contact with LEU 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I PHE* 5.1 6.1 - - + -
92I VAL* 4.4 13.9 - - + -
100I VAL* 5.2 11.0 - - + +
103I ALA* 6.4 0.2 - - + -
104I ARG* 3.3 46.0 + - + +
107I LEU* 4.0 23.6 - - + -
108I MET* 3.7 12.1 - - - +
123I VAL* 4.5 6.3 - - + -
139I ILE* 2.9 36.9 + - + +
142I LYS* 1.3 81.7 - - + +
144I GLY* 1.3 62.7 + - - +
145I LEU* 3.7 37.0 - - + +
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Residues in contact with GLY 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ARG* 4.5 6.1 - - - -
108I MET* 5.5 1.6 - - - +
140I THR 2.6 16.9 + - - -
141I ASP* 3.5 9.6 + - - -
143I LEU* 1.3 76.2 - - - +
145I LEU* 1.3 60.5 + - - -
146I HIS* 3.2 4.0 - - - -
147I SER* 2.8 28.6 + - - -
148I LEU* 4.5 3.8 - - - +
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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