Contacts of the helix formed by residues 113 - 126 (chain D) in PDB entry 1XPM
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 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C PHE* 5.9 0.4 - - - -
77D ALA* 3.5 12.3 - - + +
78D THR 4.6 0.4 - - - +
107D MET* 3.4 37.0 - - + +
108D LYS* 4.1 1.6 - - - -
109D GLU* 3.6 17.0 + - - +
111D SCY 3.7 1.6 - - - -
112D TYR* 1.3 78.7 - - - +
114D ALA* 1.3 60.7 + - - +
115D THR 3.2 0.2 - - - -
116D PRO* 3.3 23.2 - - - +
117D ALA* 3.5 9.9 + - - +
278D THR* 4.1 9.2 - - + +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ALA* 3.4 18.5 - - + +
112D TYR 3.1 3.8 + - - -
113D ALA* 1.3 75.8 - - - +
115D THR* 1.3 57.0 + - - +
117D ALA* 3.2 6.9 - - - +
118D ILE* 3.1 32.1 + - - +
135D VAL* 4.2 3.8 - - + +
137D ALA* 4.0 11.0 - - + -
160D MET* 4.6 6.5 - - + -
278D THR* 3.8 17.6 - - - +
282D TYR* 3.7 25.8 - - + -
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D TYR* 3.0 10.8 + - + -
114D ALA* 1.3 73.5 - - - +
116D PRO* 1.3 72.6 - - - +
117D ALA 3.0 1.3 + - - -
118D ILE* 3.2 3.1 + - - +
119D GLN* 3.0 28.7 + - + +
282D TYR* 2.8 22.5 + - - -
304D SER* 2.7 28.7 + - - -
312D GLU* 3.6 32.8 - - - +
314D TYR* 3.7 21.5 - - + -
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Residues in contact with PRO 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 4.3 15.7 - - - +
105C PHE* 3.8 36.1 - - + -
107D MET* 4.0 9.9 - - - -
112D TYR* 3.2 35.4 - - + +
113D ALA* 3.3 15.9 - - - +
115D THR* 1.3 91.0 - - - +
117D ALA* 1.3 54.5 + - - +
119D GLN* 4.3 6.3 - - + -
120D LEU* 2.8 39.2 + - + +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ILE* 3.9 19.2 - - + +
77D ALA* 5.1 2.7 - - + -
107D MET* 3.6 19.7 - - - -
113D ALA 3.5 10.5 - - - +
114D ALA* 3.2 12.8 + - - +
115D THR 3.0 0.4 - - - -
116D PRO* 1.3 81.9 - - - +
118D ILE* 1.3 57.4 + - - +
120D LEU 4.0 0.2 - - - -
121D ALA* 3.0 28.2 + - - +
135D VAL* 3.6 24.7 - - + +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.6 6.3 - - + -
114D ALA 3.1 15.4 + - - +
115D THR* 3.4 9.9 - - - +
117D ALA* 1.3 73.6 - - - +
119D GLN* 1.3 71.6 + - + +
121D ALA* 3.4 7.9 - - - +
122D LYS* 3.1 21.8 + - - +
135D VAL* 3.8 16.6 - - + -
160D MET* 3.7 26.2 - - + -
162D ILE* 3.9 20.0 - - + +
171D LEU* 4.0 24.0 - - + +
282D TYR* 3.7 17.0 - - + +
314D TYR* 3.6 27.4 - - + +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 3.3 36.0 + - - +
115D THR* 3.0 22.7 + - + +
116D PRO 4.0 1.3 - - - +
118D ILE* 1.3 80.4 - - + +
120D LEU* 1.3 62.8 + - - +
122D LYS* 3.3 19.5 + - - +
123D ASP* 3.2 25.3 + - - +
171D LEU* 4.3 13.8 - - - +
172D ASN 4.7 7.9 + - - +
173D GLU* 5.4 1.6 - - - +
175D ALA* 4.4 6.5 - - - +
312D GLU* 3.6 8.3 - - - +
314D TYR* 3.4 44.9 - - - +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C MET* 4.0 13.7 - - + -
75C ILE* 5.1 0.4 - - + -
103C ARG* 4.0 15.7 - - - +
105C PHE* 3.7 31.0 - - + -
107C MET* 4.8 1.8 - - + -
120C LEU* 4.1 35.7 - - + +
124C TYR* 3.8 21.1 - - + -
73D MET* 5.1 0.4 - - - -
75D ILE* 5.9 0.7 - - + -
107D MET* 4.1 11.2 - - + -
116D PRO* 2.8 24.9 + - + +
117D ALA 4.4 1.1 - - - +
119D GLN* 1.3 69.9 - - - +
121D ALA* 1.3 59.4 + - - +
123D ASP* 3.2 19.7 + - + +
124D TYR* 2.9 29.3 + - - +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D MET* 4.2 12.5 - - + +
75D ILE* 4.9 0.4 - - + +
117D ALA 3.0 20.4 + - - +
118D ILE* 3.4 10.3 - - - +
120D LEU* 1.3 76.4 - - - +
122D LYS* 1.3 64.2 + - - +
124D TYR* 3.3 4.5 + - - +
125D LEU* 3.1 28.3 + - - +
133D VAL* 3.6 31.8 - - + +
135D VAL* 4.4 0.7 - - + -
162D ILE* 4.1 11.4 - - + -
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.7 40.8 - - + +
118D ILE 3.1 12.0 + - - +
119D GLN* 3.4 16.4 - - - +
121D ALA* 1.3 78.6 - - - +
123D ASP* 1.3 65.1 + - - +
125D LEU* 3.2 11.6 + - - +
126D ALA* 3.2 10.7 + - - +
162D ILE* 4.3 3.1 - - + +
171D LEU* 3.9 39.5 - - + +
172D ASN 5.3 0.4 - - - +
173D GLU* 3.5 24.5 - - - +
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 4.8 1.2 + - - -
123C ASP* 3.7 35.1 - - + +
124C TYR* 3.5 22.5 - - - +
128C ARG* 4.4 10.0 + - - -
119D GLN* 3.2 16.5 + - - +
120D LEU* 3.2 24.9 + - + +
122D LYS* 1.3 78.5 - - - +
124D TYR* 1.3 62.8 + - - +
126D ALA* 3.3 20.9 + - - +
127D THR 4.9 0.2 + - - -
173D GLU* 4.2 15.2 - - - +
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Residues in contact with TYR 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.0 2.0 - - + -
123C ASP* 3.5 18.3 - - - +
72D GLY* 4.1 10.6 + - - -
73D MET* 3.5 35.9 - - + -
103D ARG* 3.5 30.9 - - - +
120D LEU 2.9 14.1 + - - +
121D ALA 3.3 7.0 - - - +
123D ASP* 1.3 77.7 - - - +
125D LEU* 1.3 71.8 + - + +
126D ALA 3.3 0.9 + - - -
127D THR 4.0 1.9 + - - -
128D ARG* 2.7 65.5 + - - +
131D GLU* 2.7 31.3 + - + -
133D VAL* 3.7 14.1 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.2 8.3 - - + -
121D ALA 3.1 20.0 + - - +
122D LYS 3.2 5.1 + - - +
124D TYR* 1.3 85.7 - - + +
126D ALA* 1.3 63.1 + - - +
127D THR 3.1 3.6 - - - -
128D ARG* 2.9 13.8 + - + +
131D GLU* 3.4 41.1 - - + +
132D LYS 3.9 1.8 - - - +
133D VAL* 4.0 9.9 - - + -
162D ILE* 3.5 36.8 - - + +
163D ALA* 3.8 15.7 - - - +
164D HIS* 2.7 33.4 + - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 4.2 7.1 - - - +
297B GLY* 3.8 16.5 + - - -
318B LEU 4.8 1.9 - - - +
320B GLU* 4.7 16.1 + - + +
126C ALA* 6.1 5.2 - - + -
3D ILE* 4.0 13.9 - - + -
122D LYS 3.2 8.7 + - - +
123D ASP* 3.4 17.5 - - - +
124D TYR 3.2 2.2 - - - -
125D LEU* 1.3 76.7 - - - +
127D THR* 1.3 65.9 + - + +
164D HIS* 4.3 2.8 - - - -
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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