Contacts of the helix formed by residues 102 - 116 (chain C) in PDB entry 4UI2
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 ASN 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B TRP* 4.7 0.2 - - - -
1399B SRT 3.6 18.6 + - - +
54C CYS* 3.5 28.7 - - + +
56C ILE* 4.2 4.1 - - - +
57C GLN* 6.1 0.6 - - - +
99C CYS* 3.1 26.9 + - + +
100C ARG 3.5 0.6 - - - -
101C GLY* 1.3 75.1 - - - +
103C LEU* 1.3 64.3 + - - +
104C VAL* 2.9 16.7 + - - +
105C TYR* 2.8 25.4 + - + +
106C HIS* 3.0 28.4 + - - -
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Residues in contact with LEU 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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310B TRP* 3.4 38.4 - - + -
313B TRP* 4.3 9.0 - - + -
371B MET* 4.2 11.0 - - + -
385B TYR* 4.1 21.3 - - + -
386B GLN 6.0 0.2 - - - +
388B MET* 3.8 26.0 - - + -
1399B SRT 3.9 18.8 + - - +
101C GLY 3.6 4.4 + - - -
102C ASN* 1.3 74.8 + - - +
104C VAL* 1.3 65.8 + - + +
106C HIS* 3.5 1.9 + - - +
107C SER* 3.2 22.9 + - - -
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Residues in contact with VAL 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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1399B SRT 5.9 1.8 - - - +
56C ILE* 4.1 17.0 - - + -
57C GLN* 3.9 26.0 - - - +
60C THR* 5.3 5.2 - - + +
102C ASN* 2.9 10.6 + - - +
103C LEU* 1.3 77.8 - - + +
105C TYR* 1.3 61.5 + - - +
107C SER* 2.7 21.3 + - - +
108C ALA* 2.9 18.8 + - + +
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Residues in contact with TYR 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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54C CYS* 4.4 1.8 - - - -
56C ILE* 4.1 21.5 - - + +
92C THR* 3.5 27.8 + - - -
93C GLN* 5.0 2.3 - - - +
95C THR* 4.8 0.2 - - + -
96C SER* 3.8 29.3 + - - -
99C CYS* 3.3 48.0 - - + -
100C ARG* 5.7 0.4 - - - -
102C ASN* 2.8 14.6 + - - +
103C LEU 3.2 0.2 - - - -
104C VAL* 1.3 77.3 - - - +
106C HIS* 1.3 85.2 + + - +
108C ALA* 3.0 4.0 + - - +
109C VAL* 3.0 49.2 + - + +
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Residues in contact with HIS 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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310B TRP* 3.5 10.8 + - - +
312B ASP* 5.2 2.2 - - - -
313B TRP* 3.2 65.6 - + + +
99C CYS 3.7 11.9 - - - -
100C ARG* 3.1 28.5 + - - -
102C ASN 3.0 24.2 + - - +
103C LEU 4.2 2.7 - - - +
105C TYR* 1.3 96.3 - + - +
107C SER* 1.3 59.8 + - - +
109C VAL* 3.8 5.3 - - + +
110C LEU* 3.3 29.9 + - + +
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Residues in contact with SER 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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310B TRP* 4.1 17.9 - - - +
103C LEU* 3.2 15.6 + - - -
104C VAL* 2.7 26.3 + - - +
106C HIS* 1.3 73.9 - - - +
108C ALA* 1.3 55.5 + - - +
110C LEU* 3.1 8.2 + - - +
111C GLY* 2.7 32.8 + - - -
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Residues in contact with ALA 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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56C ILE* 4.1 20.2 - - + -
88C TYR* 4.0 22.4 - - + +
92C THR* 4.9 2.9 - - + -
104C VAL* 2.9 16.3 + - + +
105C TYR 3.3 4.9 - - - +
107C SER* 1.3 81.7 + - - +
109C VAL* 1.3 53.7 + - - +
111C GLY* 3.0 3.3 + - - +
112C ILE* 2.7 41.5 + - - +
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Residues in contact with VAL 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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92C THR* 5.1 9.2 - - - +
105C TYR* 3.0 56.1 + - + +
106C HIS* 3.8 9.4 - - + +
107C SER 3.2 0.2 - - - -
108C ALA* 1.3 75.8 - - - +
110C LEU* 1.3 74.9 + - + +
112C ILE* 3.6 8.5 + - - +
113C SER* 3.3 21.5 + - - -
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Residues in contact with LEU 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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308B VAL* 3.2 28.5 - - + +
309B GLY* 3.8 12.8 - - - +
310B TRP* 3.6 26.2 - - + +
312B ASP* 5.8 2.9 - - - +
106C HIS* 3.3 14.1 - - + +
107C SER* 3.1 8.2 + - - +
109C VAL* 1.3 92.1 - - + +
111C GLY* 1.3 59.2 + - - +
113C SER* 3.2 9.2 + - - +
114C ASP* 2.9 29.3 + - - +
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Residues in contact with GLY 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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88C TYR* 6.2 0.2 - - - -
107C SER 2.7 14.9 + - - -
108C ALA* 3.0 7.1 + - - -
110C LEU* 1.3 75.1 - - - +
112C ILE* 1.3 63.1 + - - +
114C ASP* 3.4 11.3 - - - +
115C LEU* 3.3 24.4 - - - +
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Residues in contact with ILE 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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85C LEU* 3.8 17.2 - - + +
88C TYR* 3.3 47.6 - - + -
89C ALA* 3.6 28.9 - - + +
92C THR* 3.8 17.7 - - + +
108C ALA 2.7 22.2 + - - +
109C VAL* 3.9 6.3 - - - +
111C GLY* 1.3 73.4 - - - +
113C SER* 1.3 57.5 + - - +
115C LEU* 2.9 9.7 + - - +
116C MET* 2.8 50.8 + - + -
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Residues in contact with SER 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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109C VAL 3.3 9.3 + - - -
110C LEU* 3.2 19.8 + - - +
112C ILE* 1.3 78.7 - - - +
114C ASP* 1.3 60.6 + - - +
116C MET* 3.5 25.1 + - - +
117C SER* 3.7 7.8 + - - -
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Residues in contact with ASP 114 (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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110C LEU 2.9 18.4 + - - +
111C GLY* 3.4 11.2 - - - +
113C SER* 1.3 77.8 + - - +
115C LEU* 1.3 63.0 + - + +
117C SER* 2.5 27.9 + - - -
118C GLN* 3.5 20.8 + - - +
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Residues in contact with LEU 115 (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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63C PHE* 4.8 12.6 - - + -
81C PHE* 5.9 6.1 - - + -
85C LEU* 3.7 33.2 - - + +
88C TYR* 6.4 1.3 - - + -
111C GLY 3.3 17.5 - - - +
112C ILE* 2.9 7.4 + - + +
114C ASP* 1.3 79.3 - - - +
116C MET* 1.3 60.9 + - - +
117C SER 3.1 2.0 - - - -
118C GLN* 3.0 53.2 + - - +
119C ARG 3.6 2.3 - - - +
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Residues in contact with MET 116 (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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85C LEU* 3.7 38.1 - - + +
86C ARG* 3.9 14.4 - - + +
89C ALA* 3.9 8.7 - - + -
112C ILE* 2.8 28.8 + - + +
113C SER* 3.5 21.8 - - - +
115C LEU* 1.3 76.5 - - - +
117C SER* 1.3 55.6 + - - +
119C ARG 3.2 3.3 - - - +
120C ASN* 3.5 1.7 - - - +
121C CYS* 3.1 55.6 + - - +
122C SER* 4.2 9.9 - - - -
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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