Contacts of the helix formed by residues 87 - 96 (chain C) 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 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ALA 3.3 2.2 + - - -
86C LYS* 1.3 71.6 - - - +
88C ALA* 1.3 62.1 + - - +
89C ALA 3.0 4.7 - - - +
90C VAL* 2.9 17.3 + - + +
91C GLN* 2.8 15.8 - - - +
105C PHE* 3.7 21.8 - - - +
106C GLU* 3.5 11.0 - - - +
108D LYS* 3.4 26.9 - - - +
109D GLU* 3.0 19.5 + - + +
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Residues in contact with ALA 88 (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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51C ILE* 4.1 18.4 - - + -
52C VAL* 4.1 19.2 - - + +
76C VAL* 4.1 16.8 - - + -
82C VAL* 5.5 2.7 - - + -
86C LYS 3.5 1.4 + - - -
87C ALA* 1.3 71.0 - - - +
89C ALA* 1.3 62.0 + - - +
90C VAL 3.1 0.7 + - - -
91C GLN* 3.3 17.5 + - - +
92C ILE* 3.1 27.3 + - + +
106C GLU* 2.8 19.6 + - - +
138C THR* 5.7 0.2 - - + -
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Residues in contact with ALA 89 (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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74C VAL* 3.4 32.6 - - + +
76C VAL* 3.5 22.0 - - + +
87C ALA* 3.0 1.4 - - + +
88C ALA* 1.3 80.1 - - - +
90C VAL* 1.3 56.5 + - - +
92C ILE* 3.8 1.5 - - - -
93C HIS* 2.9 31.5 + - - +
104C CYS* 3.9 4.6 - - + -
105C PHE* 3.5 28.3 - - - +
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Residues in contact with VAL 90 (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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86C LYS* 4.0 7.6 - - + -
87C ALA* 2.9 17.6 + - + +
89C ALA* 1.3 75.8 - - - +
91C GLN* 1.3 68.8 + - - +
93C HIS* 3.3 7.0 + - - +
94C ASN* 3.1 20.6 + - - +
104C CYS* 4.1 11.0 - - + -
109D GLU* 4.0 15.7 - - - +
179D THR* 4.1 10.9 - - + +
181D ASP* 3.9 16.8 - - - +
308D GLY 3.4 29.4 - - - +
310D VAL* 3.9 26.5 - - + -
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Residues in contact with GLN 91 (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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52C VAL* 3.8 35.0 - - + +
82C VAL* 4.8 9.9 - - - +
83C ASP* 5.8 2.0 - - - +
86C LYS* 3.6 26.0 + - - +
87C ALA 2.8 26.3 + - - +
88C ALA* 3.3 12.0 + - - +
90C VAL* 1.3 73.4 - - - +
92C ILE* 1.3 58.6 + - - +
94C ASN* 3.2 3.3 + - - +
95C LEU* 2.8 35.3 + - + +
382C ARG* 6.2 0.8 - - - +
384C TYR* 5.0 11.9 + - + -
181D ASP* 3.4 18.6 - - - +
183D TYR* 4.0 17.8 + - - +
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Residues in contact with ILE 92 (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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51C ILE 4.5 2.2 - - - +
52C VAL* 3.8 37.0 - - + +
55C GLY* 4.1 11.0 - - - -
56C ALA* 4.4 7.0 - - + +
74C VAL* 4.8 5.4 - - + -
76C VAL* 3.9 20.9 - - + -
88C ALA* 3.1 19.7 + - + +
89C ALA* 4.0 5.2 - - - +
91C GLN* 1.3 73.6 - - - +
93C HIS* 1.3 66.9 + - - +
95C LEU* 3.3 6.0 + - - +
96C LEU* 2.9 48.5 + - + +
136C ILE* 3.6 25.8 - - + -
138C THR* 5.3 0.2 - - + -
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Residues in contact with HIS 93 (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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74C VAL* 4.0 10.3 - - + +
89C ALA 2.9 19.5 + - - +
90C VAL* 3.5 3.6 + - - +
92C ILE* 1.3 76.5 - - - +
94C ASN* 1.3 65.7 + - - +
96C LEU 4.0 0.2 - - - -
97C GLY* 3.3 2.9 + - - -
98C ILE* 3.3 69.1 + - + +
99C GLN 2.8 22.8 + - - -
100C PRO* 4.1 12.7 - - + +
102C ALA* 4.2 8.1 - - + +
104C CYS* 3.5 25.1 - - - -
179D THR* 3.9 24.2 - - - +
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Residues in contact with ASN 94 (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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90C VAL 3.1 8.6 + - - +
91C GLN 3.4 7.8 + - - +
92C ILE 3.1 0.2 - - - -
93C HIS* 1.3 81.1 + - - +
95C LEU* 1.3 68.3 + - - +
97C GLY* 3.1 14.3 + - - -
386C ARG* 4.0 19.8 + - - +
181D ASP* 3.4 37.5 + - + +
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Residues in contact with LEU 95 (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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52C VAL* 3.8 29.4 - - + +
56C ALA* 4.1 14.1 - - + -
91C GLN* 2.8 22.6 + - + +
92C ILE* 3.3 4.7 + - - +
94C ASN* 1.3 76.0 - - + +
96C LEU* 1.3 60.8 + - - +
97C GLY 3.5 0.3 + - - -
372C PHE* 3.6 46.6 - - + -
384C TYR* 4.2 24.7 - - + -
386C ARG* 3.3 44.5 + - + +
390C GLU* 6.1 0.9 - - - +
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Residues in contact with LEU 96 (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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56C ALA* 3.9 22.4 - - + +
59C ALA* 3.7 12.6 - - + -
60C LYS* 4.0 22.4 - - + -
63C ILE* 4.9 9.8 - - + +
68C LYS* 3.3 27.5 + - - +
92C ILE* 2.9 41.7 + - + +
95C LEU* 1.3 75.7 - - - +
97C GLY* 1.3 62.4 + - - +
98C ILE* 3.3 15.2 + - + -
134C LEU* 3.7 24.9 - - + -
372C PHE* 4.3 11.0 - - + -
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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