Contacts of the helix formed by residues 96 - 113 (chain C) in PDB entry 4UHY
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 ASP 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A TRP* 4.5 1.1 - - - -
383A LYS* 5.0 3.8 + - - +
48C CYS* 3.6 36.5 - - + +
50C ILE* 3.6 7.8 - - - +
93C CYS* 3.2 8.0 + - + +
94C ARG 3.6 0.8 + - - -
95C GLY* 1.4 76.1 - - - +
97C LEU* 1.3 60.0 + - - +
98C ALA* 2.9 17.2 + - - +
99C TYR* 2.8 31.7 + - + +
100C HIS* 2.7 33.8 + - - -
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Residues in contact with LEU 97 (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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310A TRP* 3.5 41.3 - - + -
313A TRP* 4.2 9.1 - - + -
371A MET* 4.0 10.3 - - + -
385A TYR* 3.5 32.6 - - + -
388A MET* 4.3 10.1 - - + -
341B ASN* 3.2 38.8 - - + +
344B ILE* 3.8 22.7 - - + -
345B VAL* 4.4 0.9 - - + -
95C GLY 4.1 2.2 + - - -
96C ASP* 1.3 71.5 + - - +
98C ALA* 1.4 60.0 + - - +
100C HIS* 3.4 2.1 + - - +
101C SER* 2.9 27.0 + - - -
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Residues in contact with ALA 98 (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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334B ALA* 3.8 29.2 - - + -
344B ILE* 4.8 8.7 - - + +
50C ILE* 4.3 13.0 - - + -
96C ASP* 2.9 8.1 + - - +
97C LEU* 1.4 75.3 - - - +
99C TYR* 1.4 55.3 - - - +
101C SER* 3.0 8.8 + - - -
102C ALA* 2.6 38.7 + - - +
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Residues in contact with TYR 99 (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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50C ILE* 3.8 30.4 - - + +
86C THR* 3.7 23.5 + - - -
87C ARG* 5.1 0.9 + - - -
89C THR* 4.4 1.3 - - + -
90C ALA* 3.4 34.0 + - - +
93C CYS* 3.2 43.1 - - + -
94C ARG* 5.4 0.9 - - - -
96C ASP* 2.8 19.5 + - + +
98C ALA* 1.4 75.9 - - - +
100C HIS* 1.3 82.1 + + - +
102C ALA* 3.4 2.6 - - - +
103C VAL* 3.0 56.3 + - + +
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Residues in contact with HIS 100 (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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310A TRP* 4.0 5.2 - - + +
312A ASP* 4.5 5.2 - - - -
313A TRP* 3.3 63.7 - + + +
93C CYS 3.6 13.2 - - - -
94C ARG* 2.9 31.1 + - - -
96C ASP 2.7 21.4 + - - +
97C LEU 3.8 3.4 - - - +
98C ALA 3.2 0.2 - - - -
99C TYR* 1.3 90.4 - + - +
101C SER* 1.4 60.9 + - - +
103C VAL* 4.0 6.0 - - + +
104C HIS* 2.9 37.6 + + + -
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Residues in contact with SER 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 4.1 12.4 - - - +
331B PHE* 3.8 13.4 - - - -
344B ILE* 3.7 28.1 + - - +
348B LEU* 5.0 8.7 - - - +
97C LEU 2.9 14.9 + - - -
98C ALA* 3.0 9.6 + - - -
100C HIS* 1.4 73.5 - - - +
102C ALA* 1.4 53.5 + - - +
104C HIS* 3.3 3.4 + - - +
105C GLY* 2.7 34.0 + - - -
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Residues in contact with ALA 102 (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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331B PHE* 3.6 14.2 - - + -
332B PRO* 6.1 0.4 - - + -
50C ILE* 4.2 17.0 - - + -
54C ASN* 6.1 0.2 - - + -
82C TYR* 3.6 20.6 - - + +
86C THR* 4.2 7.2 - - + -
98C ALA 2.6 18.6 + - - +
99C TYR 3.4 7.0 - - - +
101C SER* 1.4 68.8 - - - +
103C VAL* 1.3 52.3 + - - +
105C GLY* 2.7 22.7 + - - -
106C ILE* 2.9 23.9 + - - +
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Residues in contact with VAL 103 (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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312A ASP* 6.0 0.9 - - - +
86C THR* 3.9 16.2 - - - +
99C TYR* 3.0 54.4 + - + +
100C HIS* 4.0 8.5 - - + +
102C ALA* 1.3 74.9 - - - +
104C HIS* 1.4 64.8 + - + +
106C ILE* 3.9 10.5 + - - +
107C GLU* 3.7 26.1 + - - +
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Residues in contact with HIS 104 (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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308A VAL 3.9 7.0 + - - -
309A GLY* 3.2 32.8 + - - -
310A TRP* 3.7 18.1 - + - +
312A ASP* 2.6 34.0 + - - -
348B LEU* 5.1 11.4 - - + -
100C HIS* 2.9 32.2 + + + +
101C SER* 3.7 6.1 - - - +
103C VAL* 1.4 80.0 - - + +
105C GLY* 1.3 61.1 + - - +
107C GLU* 3.7 20.3 + - - +
108C ASP* 3.0 24.8 - - - +
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Residues in contact with GLY 105 (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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331B PHE* 3.6 25.6 - - - -
101C SER 2.7 19.5 + - - -
102C ALA 2.7 4.6 + - - -
104C HIS* 1.3 73.4 - - - +
106C ILE* 1.4 63.2 + - - +
107C GLU 3.3 0.2 - - - -
108C ASP* 3.0 19.8 + - - +
109C LEU* 3.3 13.9 + - - +
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Residues in contact with ILE 106 (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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331B PHE* 3.7 4.6 - - + -
79C LEU* 4.1 10.2 - - + +
82C TYR* 3.6 38.6 - - + -
83C ALA* 4.0 26.7 - - + -
86C THR* 3.8 34.5 - - + +
102C ALA 2.9 22.8 + - - +
103C VAL* 4.1 7.0 - - - +
105C GLY* 1.4 68.5 - - - +
107C GLU* 1.4 55.8 + - - +
109C LEU* 2.9 29.4 + - + +
110C MET* 3.0 28.8 + - + +
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Residues in contact with GLU 107 (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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103C VAL* 3.7 18.5 + - - +
104C HIS* 3.7 26.1 + - - +
106C ILE* 1.4 78.1 - - - +
108C ASP* 1.4 63.0 + - - +
110C MET* 3.3 22.8 + - + +
111C SER* 3.4 15.3 + - - +
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Residues in contact with ASP 108 (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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351B SER* 4.6 17.0 + - - +
104C HIS 3.0 17.2 - - - +
105C GLY* 3.0 12.3 + - - +
107C GLU* 1.4 78.1 - - - +
109C LEU* 1.3 65.8 + - + +
111C SER* 4.0 3.4 + - - -
112C GLN* 3.1 41.2 + - - +
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Residues in contact with LEU 109 (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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331B PHE* 3.7 33.9 - - + +
57C PHE* 4.5 19.3 - - + -
61C THR* 6.3 0.7 - - + -
79C LEU* 3.6 25.0 - - + +
82C TYR* 6.3 0.2 - - + -
105C GLY 3.6 9.4 - - - +
106C ILE* 2.9 8.9 + - + +
108C ASP* 1.3 79.8 - - + +
110C MET* 1.4 63.3 + - - +
111C SER 3.5 0.4 - - - -
112C GLN* 4.1 15.2 - - - +
113C HIS* 3.3 28.8 + - - +
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Residues in contact with MET 110 (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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79C LEU* 3.4 46.9 - - + +
80C ARG* 4.1 12.6 - - + +
83C ALA* 4.5 5.6 - - + -
106C ILE* 3.0 29.4 + - + +
107C GLU* 3.4 12.8 - - - +
108C ASP 3.3 0.2 - - - -
109C LEU* 1.4 78.0 - - - +
111C SER* 1.3 57.6 + - - +
114C ASN* 3.3 19.2 + - - -
115C CYS* 3.4 39.7 + - - +
116C SER* 6.1 1.6 - - - -
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Residues in contact with SER 111 (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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107C GLU* 3.4 14.7 + - - +
108C ASP* 4.5 4.7 - - - -
109C LEU 3.5 0.2 - - - -
110C MET* 1.3 76.6 - - - +
112C GLN* 1.4 61.3 + - - +
114C ASN* 3.0 24.7 - - - +
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Residues in contact with GLN 112 (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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108C ASP* 3.1 31.8 + - - +
109C LEU* 4.2 17.0 - - - +
110C MET 3.5 0.4 - - - -
111C SER* 1.4 79.3 - - - +
113C HIS* 1.4 59.9 + - - +
114C ASN* 3.3 6.0 + - - +
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Residues in contact with HIS 113 (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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71C ASP* 5.9 6.5 - - + -
72C THR* 3.6 24.0 - - + +
76C CYS* 4.5 2.7 - - - -
79C LEU* 5.5 3.8 - - + -
109C LEU 3.3 17.8 + - - +
112C GLN* 1.4 75.3 - - + +
114C ASN* 1.4 67.0 + - - +
115C CYS* 3.3 18.8 + - - -
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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