Contacts of the helix formed by residues 138 - 145 (chain C) in PDB entry 1XUL
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 PHE 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C LEU 4.6 6.5 - - - +
112C ARG* 5.4 5.3 + - - +
114C ILE 5.2 0.9 - - - -
116C PRO* 4.1 33.9 - - + -
119C PHE* 5.6 8.5 - + - -
128C LEU* 6.3 0.7 - - + -
130C ILE* 3.4 33.4 - - + -
135C ILE* 1.1 79.6 - - + +
137C LYS* 1.3 70.2 - - - +
139C PRO* 1.3 53.5 - - + +
140C ASP* 1.9 15.4 + - - +
141C VAL* 1.5 95.0 + - + -
144C VAL* 6.1 0.7 - - + -
145C PHE* 3.7 2.9 - + - -
155C ILE* 4.9 14.1 - - + -
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Residues in contact with PRO 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE 2.8 8.6 - - - +
136C ARG 1.7 36.6 - - - +
137C LYS* 1.9 37.7 - - - +
138C PHE* 1.3 74.9 - - + +
140C ASP* 1.4 49.6 - - - +
141C VAL* 2.7 7.4 - - + +
142C THR* 2.0 44.0 + - + +
145C PHE* 3.7 4.3 - - + -
155C ILE* 5.7 2.9 - - + -
164C ILE* 3.1 38.1 - - + -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PRO* 6.0 3.4 - - + -
120C ILE* 5.3 2.5 - - + -
137C LYS* 2.2 51.8 + - - +
138C PHE* 1.9 15.8 + - - +
139C PRO* 1.4 62.4 - - - +
141C VAL* 1.4 46.9 - - - +
142C THR* 1.7 49.0 + - - +
143C LYS* 2.3 34.3 + - + +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PRO* 5.6 1.2 - - - +
119C PHE* 6.3 0.7 - - + -
120C ILE* 4.7 3.5 - - - +
128C LEU* 6.1 2.5 - - + -
138C PHE* 1.5 118.9 + - + +
139C PRO 3.8 0.4 - - - +
140C ASP* 1.4 61.9 - - - +
142C THR* 1.3 48.2 - - - +
143C LYS 3.2 1.1 - - - -
144C VAL* 2.9 27.8 + - + +
145C PHE* 1.9 92.8 + - + -
153C LEU* 4.8 4.0 - - + -
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PRO* 2.0 34.9 + - + +
140C ASP* 1.7 43.8 + - - +
141C VAL* 1.3 61.6 - - - +
143C LYS* 1.3 73.3 + - - +
145C PHE* 2.4 17.2 + - + +
146C SER* 2.9 25.8 + - - -
164C ILE* 5.7 2.2 - - + -
166C GLY 4.5 9.9 - - - +
168C ALA* 3.3 34.2 - - + +
169C PHE* 4.6 5.8 - - + +
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Residues in contact with LYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.6 20.2 - - + +
140C ASP* 2.3 42.6 + - + +
142C THR* 1.3 74.2 + - - +
144C VAL* 1.3 60.1 + - - +
146C SER* 3.0 25.6 + - - +
147C SER* 4.5 2.4 - - - -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PRO* 5.0 0.2 - - + -
119C PHE* 4.3 17.9 - - + +
120C ILE* 1.6 94.0 - - + +
128C LEU* 5.2 1.8 - - + -
138C PHE* 6.1 0.2 - - + -
141C VAL* 2.9 22.8 + - + +
143C LYS* 1.3 75.4 - - - +
145C PHE* 1.3 59.6 - - + +
147C SER* 2.3 34.2 + - - -
150C ASN* 4.0 19.9 + - - +
153C LEU* 6.6 0.2 - - + -
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Residues in contact with PHE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PHE* 3.7 3.1 - + - -
139C PRO* 3.7 5.4 - - + -
141C VAL* 1.9 92.4 + - + -
142C THR* 2.4 18.1 + - + +
144C VAL* 1.3 72.8 - - + +
146C SER* 1.3 56.3 + - - +
147C SER* 3.3 5.7 + - - -
148C GLU 5.0 4.2 - - - +
150C ASN* 5.8 5.1 - - - +
153C LEU* 2.7 42.6 - - + -
155C ILE* 4.5 11.4 - - + -
168C ALA 5.1 3.4 - - - +
169C PHE* 3.9 37.0 - + + +
171C GLY 5.6 1.7 - - - +
172C MET 5.7 0.2 - - - +
174C ASN* 4.3 7.3 + - - +
175C GLU 5.8 0.2 + - - -
176C SER* 5.8 6.9 + - - -
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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