Contacts of the helix formed by residues 131 - 137 (chain t) in PDB entry 6QX2
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 ILE 131 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101t TYR* 4.0 24.2 - - + +
102t PRO 3.6 13.7 - - - +
103t LEU* 4.1 13.0 - - + -
129t THR* 3.1 14.6 - - - +
130t LYS* 1.3 76.0 - - - +
132t THR* 1.3 62.9 + - - +
134t GLU* 3.0 23.0 + - + +
135t LEU 3.5 2.9 + - - -
164t PHE* 3.5 32.5 - - + -
188t LEU* 4.1 11.2 - - + -
476t ILE* 6.0 0.2 - - + -
480t PHE* 3.7 48.7 - - + -
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Residues in contact with THR 132 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50t LEU* 4.0 22.9 - - + -
103t LEU* 2.6 49.9 + - - +
128t MET* 3.8 20.2 - - + -
129t THR* 3.0 12.8 + - - -
131t ILE* 1.3 75.7 - - - +
133t LEU* 1.3 65.0 + - - +
135t LEU* 3.1 18.3 + - + +
136t LEU* 3.2 23.8 + - + +
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Residues in contact with LEU 133 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54t ASN* 5.5 2.0 - - - +
59t THR* 4.4 10.3 - - + -
60t PRO* 4.0 29.2 - - + -
128t MET* 3.6 25.6 - - + -
129t THR 3.7 2.7 + - - +
130t LYS* 3.2 20.9 - - + +
131t ILE 3.2 0.2 - - - -
132t THR* 1.3 77.7 - - - +
134t GLU* 1.3 57.2 - - - +
136t LEU* 3.2 5.5 + - + +
137t ARG* 2.8 37.0 + - - +
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Residues in contact with GLU 134 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130t LYS 4.6 0.9 - - - +
131t ILE* 3.0 13.9 + - + +
133t LEU* 1.3 83.1 - - - +
135t LEU* 1.3 63.8 + - - +
136t LEU 3.5 0.3 + - - -
137t ARG* 3.7 10.6 + - - +
163t ARG* 3.0 40.7 + - + +
164t PHE* 4.0 14.6 - - + -
476t ILE* 3.6 24.2 - - + +
479t ARG* 3.3 30.6 + - - -
480t PHE* 3.7 24.9 - - + -
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Residues in contact with LEU 135 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40t ASP* 4.5 5.6 - - + +
42t LEU* 4.5 5.8 - - + -
50t LEU* 3.6 27.4 - - + -
103t LEU* 3.8 27.1 - - + -
131t ILE 3.5 2.7 + - - +
132t THR* 3.1 13.3 + - + +
134t GLU* 1.3 78.3 - - - +
136t LEU* 1.3 59.1 + - + +
137t ARG 3.5 0.2 - - - -
160t LEU* 3.5 14.4 - - + +
161t PRO* 3.4 11.1 - - - +
162t ALA* 2.9 43.7 + - + +
164t PHE* 3.6 23.3 - - + +
166t ASN* 3.9 24.2 - - + +
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Residues in contact with LEU 136 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50t LEU* 3.7 17.0 - - + +
51t TYR* 4.4 5.2 - - - -
54t ASN* 3.7 38.4 - - + +
128t MET* 3.7 20.6 - - - -
132t THR* 3.2 24.7 + - + +
133t LEU* 3.5 5.2 - - + +
135t LEU* 1.3 77.6 - - + +
137t ARG* 1.3 67.2 + - - +
138t ASP 3.2 0.5 + - - -
139t ILE* 3.0 44.4 + - + +
160t LEU* 3.9 25.4 - - + -
161t PRO* 4.2 3.8 - - - -
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Residues in contact with ARG 137 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133t LEU 2.8 15.8 + - - +
134t GLU* 3.7 11.9 + - - +
135t LEU 3.5 1.8 - - - -
136t LEU* 1.3 74.2 - - - +
138t ASP* 1.3 75.1 + - - +
161t PRO* 3.2 22.7 - - - +
163t ARG* 3.9 20.7 - - + +
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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