Contacts of the helix formed by residues 135 - 143 (chain F) in PDB entry 1XBT
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 135 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F GLN 5.0 2.6 + - - -
102F PHE 5.5 2.1 + - - +
103F PRO* 4.9 11.9 - - + +
105F ILE* 4.5 16.0 - - + +
106F VAL* 3.8 10.6 - - + +
107F GLU* 6.2 0.2 - - - +
134F GLY* 1.3 73.3 - - - -
136F ILE* 1.3 63.3 + - - +
137F LEU 3.3 2.7 - - - -
138F ASN* 3.1 39.0 + - - +
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 4.2 15.5 - - + -
25F LEU* 4.4 4.0 - - + +
99F GLY* 4.0 7.2 - - - +
100F GLN* 3.9 15.9 - - - +
105F ILE* 4.5 8.8 - - + +
121F VAL* 4.4 3.6 - - + -
123F ALA* 3.6 28.9 - - + -
124F LEU 3.5 22.7 - - - +
125F ASP* 4.5 3.6 - - - +
133F PHE 3.6 14.4 - - - +
134F GLY 3.4 2.8 + - - -
135F ALA* 1.3 78.6 - - - +
137F LEU* 1.3 80.7 + - + +
139F LEU* 3.1 38.5 + - + +
140F VAL* 4.3 2.1 + - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 4.6 4.3 - - + -
125F ASP* 4.2 13.5 - - + +
132F PRO* 4.1 23.1 - - + -
133F PHE 6.0 0.2 - - - +
134F GLY 5.1 1.2 + - - -
135F ALA 3.1 1.4 + - - -
136F ILE* 1.3 87.7 - - + +
138F ASN* 1.3 56.7 + - - +
139F LEU 3.0 5.6 - - - -
140F VAL* 3.1 30.7 + - + +
137H LEU* 3.1 59.2 - - + +
138H ASN* 5.3 0.2 - - - +
140H VAL* 4.1 21.3 - - + -
141H PRO* 3.8 22.2 - - + -
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Residues in contact with ASN 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F VAL* 3.6 18.2 - - + +
135F ALA* 3.1 33.8 + - - +
137F LEU* 1.3 77.6 - - - +
139F LEU* 1.3 58.9 + - - +
140F VAL 3.3 0.2 - - - -
141F PRO* 3.3 13.0 - - - +
142F LEU* 3.4 17.8 - - - +
130H ARG 5.5 0.2 - - - +
132H PRO* 3.8 25.5 - - + +
137H LEU* 5.4 0.2 - - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 4.0 20.2 - - + -
23F VAL* 4.1 17.0 - - + -
105F ILE* 4.0 17.7 - - + -
106F VAL* 4.3 16.8 - - + +
109F CYS* 3.8 25.4 - - + -
121F VAL* 3.9 26.0 - - + -
135F ALA 4.2 0.4 + - - -
136F ILE* 3.1 34.7 + - + +
137F LEU 3.0 0.4 - - - -
138F ASN* 1.3 79.2 - - - +
140F VAL* 1.3 59.1 + - - +
141F PRO 3.4 0.2 - - - -
142F LEU* 2.9 26.7 + - + +
143F ALA* 3.0 14.6 + - - +
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 5.3 4.5 - - + -
25F LEU* 4.7 7.9 - - + -
136F ILE 4.8 1.8 - - - +
137F LEU* 3.1 33.0 + - + +
139F LEU* 1.3 76.3 - - + +
141F PRO* 1.3 62.3 - - + +
142F LEU 3.2 0.9 + - - -
143F ALA* 3.2 6.8 + - - +
146F VAL* 4.2 32.9 - - + +
25H LEU* 3.9 20.0 - - + -
125H ASP* 3.9 7.6 - - + +
137H LEU* 3.8 24.0 - - + -
140H VAL* 5.5 3.4 - - + -
148H LYS* 3.0 24.5 + - + -
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Residues in contact with PRO 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F LEU 3.5 7.2 - - - +
138F ASN 3.3 15.5 - - - +
140F VAL* 1.3 94.3 - - + +
142F LEU* 1.3 56.4 + - - -
143F ALA 3.5 0.2 - - - -
125H ASP* 3.5 22.9 - - - +
126H GLY* 3.9 14.7 - - - -
130H ARG* 3.6 31.5 - - - +
132H PRO* 3.8 24.7 - - + -
137H LEU* 3.9 8.3 - - + -
148H LYS* 4.4 1.1 + - - -
162H TYR* 3.4 22.1 - - - -
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.8 8.3 - - + +
106F VAL* 3.8 24.9 - - + -
110F GLU* 4.1 21.8 - - + +
138F ASN 3.4 20.9 - - - +
139F LEU* 2.9 17.9 + - + +
141F PRO* 1.3 76.7 - - - +
143F ALA* 1.3 55.9 + - - +
130H ARG* 3.4 54.5 + - + +
162H TYR* 2.7 23.6 + - - -
186H ARG* 2.8 17.7 + - - -
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Residues in contact with ALA 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.6 18.6 - - + +
23F VAL* 3.7 23.3 - - + -
139F LEU 3.0 12.7 + - - +
140F VAL 3.2 2.3 + - - +
141F PRO 3.5 0.2 - - - -
142F LEU* 1.3 79.5 - - - +
144F GLU* 1.3 61.8 + - - +
145F SER 3.3 1.8 - - - +
146F VAL* 3.8 18.6 - - + -
148H LYS* 2.7 29.8 + - - -
161H ALA* 3.9 3.1 - - - +
162H TYR* 3.8 2.4 - - - -
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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